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Delete PTL2/Scripts-DEV directory
This commit is contained in:
Auden Cote-L'Heureux
GitHub
parent
63d574c64f
commit
7d513beb64
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PTL2/Scripts-DEV/.DS_Store
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PTL2/Scripts-DEV/.DS_Store
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PTL2/Scripts-DEV/Guidance_EXAMPLE/.DS_Store
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@ -1,30 +0,0 @@
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import os,sys
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with open('ScoreBySeq.tsv', 'w') as o:
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for clade in os.listdir('GuidanceOutput'):
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if(os.path.isfile('GuidanceOutput/' + clade + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names')):
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for line in open('GuidanceOutput/' + clade + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names'):
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if('SEQUENCE_NAME' not in line):
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o.write(line)
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@ -1,16 +0,0 @@
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import os, sys
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from Bio import SeqIO
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score_by_seq = { line.split('\t')[0] : float(line.split('\t')[1]) for line in open('ScoreBySeq.tsv') }
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remove3 = [seq for seq in score_by_seq if score_by_seq[seq] < 0.3]
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remove5 = [seq for seq in score_by_seq if score_by_seq[seq] < 0.5]
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remove7 = [seq for seq in score_by_seq if score_by_seq[seq] < 0.7]
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for clade in os.listdir('GuidanceOutput'):
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if('OG5_' in clade):
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with open('SeqFiltered_ToAlign/Preguidance_0.7/' + clade[:12] + '.fasta', 'w') as o:
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for rec in SeqIO.parse('GuidanceOutput/' + clade + '/Seqs.Orig.fas', 'fasta'):
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if(rec.id not in remove7):
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o.write('>' + rec.id + '\n' + str(rec.seq) + '\n\n')
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@ -1,170 +0,0 @@
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--- init HoT_COS_GUIDANCE2.pl pid=6505 Sun Feb 20 00:14:47 2022
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met=MFT
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infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
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seqtype=0
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outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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tgz=0
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debug=0
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basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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output_id=MSA_0_cos_MFT
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---
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TREE_FILE:MSA.MAFFT.semphy.tree_0.rooted.GoodBranchLength
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-Making hot_H ...
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-Making hot_T ...
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-Making branch 20 of 125 ...
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---
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MSA_0_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_0_cos_MFT
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Sun Feb 20 00:14:53 2022
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--- init HoT_COS_GUIDANCE2.pl pid=10893 Sun Feb 20 00:14:53 2022
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met=MFT
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infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
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seqtype=0
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outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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tgz=0
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debug=0
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basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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output_id=MSA_1_cos_MFT
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---
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TREE_FILE:MSA.MAFFT.semphy.tree_1.rooted.GoodBranchLength
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-Making hot_H ...
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-Making hot_T ...
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-Making branch 109 of 125 ...
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---
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MSA_1_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_1_cos_MFT
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Sun Feb 20 00:15:00 2022
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--- init HoT_COS_GUIDANCE2.pl pid=14766 Sun Feb 20 00:15:00 2022
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met=MFT
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infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
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seqtype=0
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outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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tgz=0
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debug=0
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basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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output_id=MSA_2_cos_MFT
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---
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TREE_FILE:MSA.MAFFT.semphy.tree_2.rooted.GoodBranchLength
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-Making hot_H ...
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-Making hot_T ...
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-Making branch 83 of 125 ...
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---
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MSA_2_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_2_cos_MFT
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Sun Feb 20 00:15:07 2022
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--- init HoT_COS_GUIDANCE2.pl pid=18991 Sun Feb 20 00:15:07 2022
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met=MFT
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infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
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seqtype=0
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outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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tgz=0
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debug=0
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basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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output_id=MSA_3_cos_MFT
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---
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TREE_FILE:MSA.MAFFT.semphy.tree_3.rooted.GoodBranchLength
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-Making hot_H ...
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-Making hot_T ...
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-Making branch 61 of 125 ...
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---
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MSA_3_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_3_cos_MFT
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Sun Feb 20 00:15:12 2022
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--- init HoT_COS_GUIDANCE2.pl pid=23356 Sun Feb 20 00:15:12 2022
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met=MFT
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infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
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seqtype=0
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outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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tgz=0
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debug=0
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basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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output_id=MSA_4_cos_MFT
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---
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TREE_FILE:MSA.MAFFT.semphy.tree_4.rooted.GoodBranchLength
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-Making hot_H ...
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-Making hot_T ...
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-Making branch 77 of 125 ...
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---
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MSA_4_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_4_cos_MFT
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Sun Feb 20 00:15:19 2022
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--- init HoT_COS_GUIDANCE2.pl pid=29089 Sun Feb 20 00:15:19 2022
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met=MFT
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infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
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seqtype=0
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outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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tgz=0
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debug=0
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basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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output_id=MSA_5_cos_MFT
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---
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TREE_FILE:MSA.MAFFT.semphy.tree_5.rooted.GoodBranchLength
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-Making hot_H ...
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-Making hot_T ...
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-Making branch 54 of 125 ...
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---
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MSA_5_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_5_cos_MFT
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Sun Feb 20 00:15:25 2022
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--- init HoT_COS_GUIDANCE2.pl pid=33605 Sun Feb 20 00:15:25 2022
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met=MFT
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infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
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seqtype=0
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outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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tgz=0
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debug=0
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basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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output_id=MSA_6_cos_MFT
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---
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TREE_FILE:MSA.MAFFT.semphy.tree_6.rooted.GoodBranchLength
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-Making hot_H ...
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-Making hot_T ...
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-Making branch 58 of 125 ...
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---
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MSA_6_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_6_cos_MFT
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Sun Feb 20 00:15:30 2022
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--- init HoT_COS_GUIDANCE2.pl pid=37939 Sun Feb 20 00:15:30 2022
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met=MFT
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infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
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seqtype=0
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outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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tgz=0
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debug=0
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basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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output_id=MSA_7_cos_MFT
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---
|
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TREE_FILE:MSA.MAFFT.semphy.tree_7.rooted.GoodBranchLength
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-Making hot_H ...
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-Making hot_T ...
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-Making branch 101 of 125 ...
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---
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MSA_7_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_7_cos_MFT
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Sun Feb 20 00:15:36 2022
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--- init HoT_COS_GUIDANCE2.pl pid=43234 Sun Feb 20 00:15:36 2022
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met=MFT
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infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
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seqtype=0
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outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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tgz=0
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debug=0
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basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
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output_id=MSA_8_cos_MFT
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---
|
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TREE_FILE:MSA.MAFFT.semphy.tree_8.rooted.GoodBranchLength
|
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-Making hot_H ...
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-Making hot_T ...
|
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-Making branch 73 of 125 ...
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---
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MSA_8_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_8_cos_MFT
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Sun Feb 20 00:15:44 2022
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--- init HoT_COS_GUIDANCE2.pl pid=49264 Sun Feb 20 00:15:45 2022
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met=MFT
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infile=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas
|
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seqtype=0
|
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outdir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
|
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tgz=0
|
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debug=0
|
||||
basedir=/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance
|
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output_id=MSA_9_cos_MFT
|
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---
|
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TREE_FILE:MSA.MAFFT.semphy.tree_9.rooted.GoodBranchLength
|
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-Making hot_H ...
|
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-Making hot_T ...
|
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-Making branch 25 of 125 ...
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---
|
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MSA_9_cos_MFT HoT_COS_GUIDANCE2.pl done : dir saved to /scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA_9_cos_MFT
|
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Sun Feb 20 00:15:50 2022
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Binary file not shown.
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File diff suppressed because it is too large
Load Diff
@ -1,353 +0,0 @@
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#COL_NUMBER #COL_SCORE
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1 0.000000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
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|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.000000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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|
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|
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|
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|
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|
||||
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|
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|
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|
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|
||||
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|
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|
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|
||||
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|
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|
||||
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|
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|
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|
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|
||||
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|
||||
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|
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|
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|
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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|
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|
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|
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||||
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|
||||
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|
||||
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|
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|
||||
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||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
148 0.000000
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
155 0.000000
|
||||
156 0.000000
|
||||
157 0.000000
|
||||
158 0.000000
|
||||
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|
||||
160 0.000000
|
||||
161 0.000000
|
||||
162 0.000000
|
||||
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|
||||
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|
||||
165 0.000000
|
||||
166 0.000000
|
||||
167 0.000000
|
||||
168 0.000000
|
||||
169 0.000000
|
||||
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|
||||
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|
||||
172 0.000000
|
||||
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|
||||
174 0.000000
|
||||
175 0.000000
|
||||
176 0.000000
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
181 0.000000
|
||||
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|
||||
183 0.000000
|
||||
184 0.000000
|
||||
185 0.000000
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
286 0.000000
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||||
287 0.000000
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||||
288 0.000000
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||||
289 0.000000
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||||
290 0.000000
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||||
291 0.000000
|
||||
292 0.000000
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||||
293 0.000000
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||||
294 0.000000
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||||
295 0.000000
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||||
296 0.000000
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||||
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||||
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||||
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||||
301 0.000000
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||||
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||||
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||||
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||||
305 0.000000
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||||
306 0.000000
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||||
307 0.000000
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||||
308 0.000000
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||||
309 0.000000
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||||
310 0.000000
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||||
311 0.000000
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||||
312 0.000000
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||||
313 0.000000
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||||
314 0.000000
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||||
315 0.000000
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||||
316 0.000000
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||||
317 0.000000
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||||
318 0.000000
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||||
319 0.000000
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||||
320 0.000000
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||||
321 0.000000
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||||
322 0.000000
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||||
323 0.000000
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||||
324 0.000000
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||||
325 0.000000
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||||
326 0.000000
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||||
327 0.000000
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||||
328 0.000000
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||||
329 0.000000
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||||
330 0.000000
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||||
331 0.000000
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||||
332 0.000000
|
||||
333 0.000000
|
||||
334 0.000000
|
||||
335 0.000000
|
||||
336 0.000000
|
||||
337 0.000000
|
||||
338 0.000000
|
||||
339 0.000000
|
||||
340 0.225000
|
||||
341 0.225000
|
||||
342 0.225000
|
||||
343 0.225000
|
||||
344 0.325000
|
||||
345 0.325000
|
||||
346 0.325000
|
||||
347 0.275000
|
||||
348 0.275000
|
||||
349 0.275000
|
||||
350 0.325000
|
||||
351 0.325000
|
||||
#END
|
||||
@ -1,6 +0,0 @@
|
||||
#REF_FILE /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.aln
|
||||
#ROWS 64 #COLUMNS 351
|
||||
#ALT_FILES -d /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/GUIDANCE2_MSA/
|
||||
#N_ALT 40
|
||||
#MEAN_RES_PAIR_SCORE 0.948841 #MEAN_COL_SCORE 0.009544
|
||||
#END
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,346 +0,0 @@
|
||||
#COL_NUMBER #RES_PAIR_COLUMN_SCORE
|
||||
1 1.000000
|
||||
2 1.000000
|
||||
3 1.000000
|
||||
4 1.000000
|
||||
7 0.924242
|
||||
8 0.969697
|
||||
9 0.969697
|
||||
10 1.000000
|
||||
11 1.000000
|
||||
12 1.000000
|
||||
13 1.000000
|
||||
14 1.000000
|
||||
15 1.000000
|
||||
16 1.000000
|
||||
17 1.000000
|
||||
18 1.000000
|
||||
19 1.000000
|
||||
20 1.000000
|
||||
21 1.000000
|
||||
22 1.000000
|
||||
23 1.000000
|
||||
24 1.000000
|
||||
25 1.000000
|
||||
26 0.971795
|
||||
27 1.000000
|
||||
28 1.000000
|
||||
29 1.000000
|
||||
30 1.000000
|
||||
31 1.000000
|
||||
32 1.000000
|
||||
33 1.000000
|
||||
34 1.000000
|
||||
35 1.000000
|
||||
36 1.000000
|
||||
37 1.000000
|
||||
38 1.000000
|
||||
39 1.000000
|
||||
40 1.000000
|
||||
41 1.000000
|
||||
42 1.000000
|
||||
43 1.000000
|
||||
44 1.000000
|
||||
45 1.000000
|
||||
46 1.000000
|
||||
47 1.000000
|
||||
48 0.963333
|
||||
49 0.963333
|
||||
50 0.963333
|
||||
51 0.963333
|
||||
52 0.969444
|
||||
53 0.955556
|
||||
54 0.955556
|
||||
55 0.955556
|
||||
56 0.955556
|
||||
57 0.955556
|
||||
58 0.955556
|
||||
59 0.955556
|
||||
60 0.955556
|
||||
61 0.955556
|
||||
62 0.960000
|
||||
63 0.960000
|
||||
64 0.960000
|
||||
65 0.960000
|
||||
66 0.961905
|
||||
67 0.961905
|
||||
68 0.954762
|
||||
69 0.950000
|
||||
70 0.945238
|
||||
71 0.942857
|
||||
72 0.942857
|
||||
73 0.942857
|
||||
74 0.942857
|
||||
75 0.942857
|
||||
76 0.942857
|
||||
77 0.925714
|
||||
78 0.856190
|
||||
79 0.936842
|
||||
80 0.936842
|
||||
81 0.936842
|
||||
82 0.936842
|
||||
83 0.936842
|
||||
84 0.906667
|
||||
85 0.942857
|
||||
86 0.942857
|
||||
87 0.942857
|
||||
88 0.945455
|
||||
89 0.945455
|
||||
90 0.945455
|
||||
91 0.945455
|
||||
92 0.945455
|
||||
93 0.945455
|
||||
94 0.945455
|
||||
95 0.945455
|
||||
96 0.945455
|
||||
97 0.945455
|
||||
98 0.945455
|
||||
99 0.945455
|
||||
100 0.945455
|
||||
101 0.945455
|
||||
102 0.945455
|
||||
103 0.945455
|
||||
104 0.945455
|
||||
105 0.945455
|
||||
106 0.945455
|
||||
107 0.945455
|
||||
108 0.945455
|
||||
109 0.945455
|
||||
110 0.950000
|
||||
111 0.919203
|
||||
112 0.945455
|
||||
113 0.945455
|
||||
114 0.945455
|
||||
115 0.945455
|
||||
116 0.940909
|
||||
117 1.000000
|
||||
118 1.000000
|
||||
119 1.000000
|
||||
120 0.909091
|
||||
121 0.909091
|
||||
122 1.000000
|
||||
123 1.000000
|
||||
124 1.000000
|
||||
125 1.000000
|
||||
126 1.000000
|
||||
127 1.000000
|
||||
128 1.000000
|
||||
129 1.000000
|
||||
130 1.000000
|
||||
131 1.000000
|
||||
132 1.000000
|
||||
133 1.000000
|
||||
134 1.000000
|
||||
135 1.000000
|
||||
136 1.000000
|
||||
137 1.000000
|
||||
138 0.982684
|
||||
139 0.982684
|
||||
140 0.952964
|
||||
141 0.904167
|
||||
142 0.854654
|
||||
143 0.837143
|
||||
144 0.703801
|
||||
145 1.000000
|
||||
146 1.000000
|
||||
147 0.984211
|
||||
148 0.948718
|
||||
149 0.948718
|
||||
150 0.948718
|
||||
151 0.948718
|
||||
152 0.948718
|
||||
153 0.948718
|
||||
154 0.948718
|
||||
156 0.948718
|
||||
157 0.948718
|
||||
158 0.948718
|
||||
159 0.948718
|
||||
160 0.948718
|
||||
161 0.950000
|
||||
162 0.950000
|
||||
163 0.937317
|
||||
164 0.938792
|
||||
165 0.938792
|
||||
166 0.940199
|
||||
167 0.940199
|
||||
168 0.940199
|
||||
169 0.940199
|
||||
170 0.940253
|
||||
171 0.940253
|
||||
172 0.940253
|
||||
173 0.941522
|
||||
174 0.941522
|
||||
175 0.941522
|
||||
176 0.941522
|
||||
177 0.941522
|
||||
178 0.941522
|
||||
179 0.946102
|
||||
180 0.946102
|
||||
181 0.946102
|
||||
182 0.946102
|
||||
183 0.946102
|
||||
184 0.946102
|
||||
185 0.946102
|
||||
186 0.946102
|
||||
187 0.946102
|
||||
188 0.902429
|
||||
189 0.821266
|
||||
190 0.715856
|
||||
191 0.639517
|
||||
192 1.000000
|
||||
193 0.713333
|
||||
194 0.693407
|
||||
195 0.891209
|
||||
196 0.938667
|
||||
197 0.927866
|
||||
198 0.927866
|
||||
199 0.927866
|
||||
200 0.927866
|
||||
201 0.927866
|
||||
202 0.927866
|
||||
203 0.924165
|
||||
204 0.923690
|
||||
205 0.926299
|
||||
206 0.924578
|
||||
207 0.907477
|
||||
208 0.898403
|
||||
209 0.917647
|
||||
210 0.949911
|
||||
211 0.932707
|
||||
212 0.932707
|
||||
213 0.932707
|
||||
214 0.933817
|
||||
215 0.930395
|
||||
216 0.930395
|
||||
217 0.933729
|
||||
218 0.937062
|
||||
219 0.937062
|
||||
220 0.937062
|
||||
221 0.937062
|
||||
222 0.937062
|
||||
223 0.937062
|
||||
224 0.937062
|
||||
225 0.937062
|
||||
226 0.933729
|
||||
227 0.933729
|
||||
228 0.933729
|
||||
229 0.933729
|
||||
230 0.935395
|
||||
231 0.937062
|
||||
232 0.937062
|
||||
233 0.877631
|
||||
234 0.877631
|
||||
235 0.877631
|
||||
236 0.877631
|
||||
237 0.877631
|
||||
238 0.877631
|
||||
239 0.877631
|
||||
240 0.877631
|
||||
241 0.880751
|
||||
242 0.880751
|
||||
243 0.880751
|
||||
244 0.880751
|
||||
245 0.880751
|
||||
247 0.874564
|
||||
248 0.874564
|
||||
249 0.874564
|
||||
250 0.714286
|
||||
253 0.934754
|
||||
254 0.934754
|
||||
255 0.938033
|
||||
256 0.938033
|
||||
257 0.938033
|
||||
258 0.938033
|
||||
259 0.941311
|
||||
260 0.941311
|
||||
261 0.941311
|
||||
262 0.941311
|
||||
263 0.938033
|
||||
264 0.934754
|
||||
265 0.934754
|
||||
266 0.934754
|
||||
267 0.934754
|
||||
268 0.934754
|
||||
269 0.934754
|
||||
270 0.934754
|
||||
271 0.975820
|
||||
272 0.983607
|
||||
273 0.990164
|
||||
274 0.990164
|
||||
275 0.990164
|
||||
277 0.990164
|
||||
278 0.990164
|
||||
279 0.990164
|
||||
280 0.990164
|
||||
281 0.990164
|
||||
282 0.990164
|
||||
283 0.990164
|
||||
284 0.990164
|
||||
285 0.990164
|
||||
286 0.928315
|
||||
287 0.931388
|
||||
288 0.961396
|
||||
289 0.930927
|
||||
290 0.930927
|
||||
291 0.930927
|
||||
292 0.993443
|
||||
293 0.993443
|
||||
294 0.993443
|
||||
295 0.993443
|
||||
296 0.993443
|
||||
297 0.993443
|
||||
298 0.993443
|
||||
299 0.993443
|
||||
300 0.993443
|
||||
301 0.993443
|
||||
302 0.996721
|
||||
303 1.000000
|
||||
304 1.000000
|
||||
305 1.000000
|
||||
306 1.000000
|
||||
307 1.000000
|
||||
308 1.000000
|
||||
309 1.000000
|
||||
310 1.000000
|
||||
311 1.000000
|
||||
312 1.000000
|
||||
313 1.000000
|
||||
314 1.000000
|
||||
315 1.000000
|
||||
316 1.000000
|
||||
317 1.000000
|
||||
318 0.967213
|
||||
319 0.936013
|
||||
320 0.936013
|
||||
321 0.936013
|
||||
322 0.967213
|
||||
323 0.967213
|
||||
324 0.967213
|
||||
325 0.967213
|
||||
326 0.944945
|
||||
327 0.894737
|
||||
328 0.967213
|
||||
329 0.967213
|
||||
330 0.967213
|
||||
331 0.967213
|
||||
332 0.967213
|
||||
333 0.966667
|
||||
334 0.966667
|
||||
335 0.966667
|
||||
336 0.966102
|
||||
337 0.966102
|
||||
338 0.966102
|
||||
339 0.965517
|
||||
340 1.000000
|
||||
341 1.000000
|
||||
342 1.000000
|
||||
343 1.000000
|
||||
344 1.000000
|
||||
345 1.000000
|
||||
346 1.000000
|
||||
347 0.990323
|
||||
348 1.000000
|
||||
349 1.000000
|
||||
350 0.951111
|
||||
351 1.000000
|
||||
#END
|
||||
@ -1,345 +0,0 @@
|
||||
#COL_NUMBER,#RES_PAIR_COLUMN_SCORE
|
||||
1,1.000000
|
||||
2,1.000000
|
||||
3,1.000000
|
||||
4,1.000000
|
||||
7,0.924242
|
||||
8,0.969697
|
||||
9,0.969697
|
||||
10,1.000000
|
||||
11,1.000000
|
||||
12,1.000000
|
||||
13,1.000000
|
||||
14,1.000000
|
||||
15,1.000000
|
||||
16,1.000000
|
||||
17,1.000000
|
||||
18,1.000000
|
||||
19,1.000000
|
||||
20,1.000000
|
||||
21,1.000000
|
||||
22,1.000000
|
||||
23,1.000000
|
||||
24,1.000000
|
||||
25,1.000000
|
||||
26,0.971795
|
||||
27,1.000000
|
||||
28,1.000000
|
||||
29,1.000000
|
||||
30,1.000000
|
||||
31,1.000000
|
||||
32,1.000000
|
||||
33,1.000000
|
||||
34,1.000000
|
||||
35,1.000000
|
||||
36,1.000000
|
||||
37,1.000000
|
||||
38,1.000000
|
||||
39,1.000000
|
||||
40,1.000000
|
||||
41,1.000000
|
||||
42,1.000000
|
||||
43,1.000000
|
||||
44,1.000000
|
||||
45,1.000000
|
||||
46,1.000000
|
||||
47,1.000000
|
||||
48,0.963333
|
||||
49,0.963333
|
||||
50,0.963333
|
||||
51,0.963333
|
||||
52,0.969444
|
||||
53,0.955556
|
||||
54,0.955556
|
||||
55,0.955556
|
||||
56,0.955556
|
||||
57,0.955556
|
||||
58,0.955556
|
||||
59,0.955556
|
||||
60,0.955556
|
||||
61,0.955556
|
||||
62,0.960000
|
||||
63,0.960000
|
||||
64,0.960000
|
||||
65,0.960000
|
||||
66,0.961905
|
||||
67,0.961905
|
||||
68,0.954762
|
||||
69,0.950000
|
||||
70,0.945238
|
||||
71,0.942857
|
||||
72,0.942857
|
||||
73,0.942857
|
||||
74,0.942857
|
||||
75,0.942857
|
||||
76,0.942857
|
||||
77,0.925714
|
||||
78,0.856190
|
||||
79,0.936842
|
||||
80,0.936842
|
||||
81,0.936842
|
||||
82,0.936842
|
||||
83,0.936842
|
||||
84,0.906667
|
||||
85,0.942857
|
||||
86,0.942857
|
||||
87,0.942857
|
||||
88,0.945455
|
||||
89,0.945455
|
||||
90,0.945455
|
||||
91,0.945455
|
||||
92,0.945455
|
||||
93,0.945455
|
||||
94,0.945455
|
||||
95,0.945455
|
||||
96,0.945455
|
||||
97,0.945455
|
||||
98,0.945455
|
||||
99,0.945455
|
||||
100,0.945455
|
||||
101,0.945455
|
||||
102,0.945455
|
||||
103,0.945455
|
||||
104,0.945455
|
||||
105,0.945455
|
||||
106,0.945455
|
||||
107,0.945455
|
||||
108,0.945455
|
||||
109,0.945455
|
||||
110,0.950000
|
||||
111,0.919203
|
||||
112,0.945455
|
||||
113,0.945455
|
||||
114,0.945455
|
||||
115,0.945455
|
||||
116,0.940909
|
||||
117,1.000000
|
||||
118,1.000000
|
||||
119,1.000000
|
||||
120,0.909091
|
||||
121,0.909091
|
||||
122,1.000000
|
||||
123,1.000000
|
||||
124,1.000000
|
||||
125,1.000000
|
||||
126,1.000000
|
||||
127,1.000000
|
||||
128,1.000000
|
||||
129,1.000000
|
||||
130,1.000000
|
||||
131,1.000000
|
||||
132,1.000000
|
||||
133,1.000000
|
||||
134,1.000000
|
||||
135,1.000000
|
||||
136,1.000000
|
||||
137,1.000000
|
||||
138,0.982684
|
||||
139,0.982684
|
||||
140,0.952964
|
||||
141,0.904167
|
||||
142,0.854654
|
||||
143,0.837143
|
||||
144,0.703801
|
||||
145,1.000000
|
||||
146,1.000000
|
||||
147,0.984211
|
||||
148,0.948718
|
||||
149,0.948718
|
||||
150,0.948718
|
||||
151,0.948718
|
||||
152,0.948718
|
||||
153,0.948718
|
||||
154,0.948718
|
||||
156,0.948718
|
||||
157,0.948718
|
||||
158,0.948718
|
||||
159,0.948718
|
||||
160,0.948718
|
||||
161,0.950000
|
||||
162,0.950000
|
||||
163,0.937317
|
||||
164,0.938792
|
||||
165,0.938792
|
||||
166,0.940199
|
||||
167,0.940199
|
||||
168,0.940199
|
||||
169,0.940199
|
||||
170,0.940253
|
||||
171,0.940253
|
||||
172,0.940253
|
||||
173,0.941522
|
||||
174,0.941522
|
||||
175,0.941522
|
||||
176,0.941522
|
||||
177,0.941522
|
||||
178,0.941522
|
||||
179,0.946102
|
||||
180,0.946102
|
||||
181,0.946102
|
||||
182,0.946102
|
||||
183,0.946102
|
||||
184,0.946102
|
||||
185,0.946102
|
||||
186,0.946102
|
||||
187,0.946102
|
||||
188,0.902429
|
||||
189,0.821266
|
||||
190,0.715856
|
||||
191,0.639517
|
||||
192,1.000000
|
||||
193,0.713333
|
||||
194,0.693407
|
||||
195,0.891209
|
||||
196,0.938667
|
||||
197,0.927866
|
||||
198,0.927866
|
||||
199,0.927866
|
||||
200,0.927866
|
||||
201,0.927866
|
||||
202,0.927866
|
||||
203,0.924165
|
||||
204,0.923690
|
||||
205,0.926299
|
||||
206,0.924578
|
||||
207,0.907477
|
||||
208,0.898403
|
||||
209,0.917647
|
||||
210,0.949911
|
||||
211,0.932707
|
||||
212,0.932707
|
||||
213,0.932707
|
||||
214,0.933817
|
||||
215,0.930395
|
||||
216,0.930395
|
||||
217,0.933729
|
||||
218,0.937062
|
||||
219,0.937062
|
||||
220,0.937062
|
||||
221,0.937062
|
||||
222,0.937062
|
||||
223,0.937062
|
||||
224,0.937062
|
||||
225,0.937062
|
||||
226,0.933729
|
||||
227,0.933729
|
||||
228,0.933729
|
||||
229,0.933729
|
||||
230,0.935395
|
||||
231,0.937062
|
||||
232,0.937062
|
||||
233,0.877631
|
||||
234,0.877631
|
||||
235,0.877631
|
||||
236,0.877631
|
||||
237,0.877631
|
||||
238,0.877631
|
||||
239,0.877631
|
||||
240,0.877631
|
||||
241,0.880751
|
||||
242,0.880751
|
||||
243,0.880751
|
||||
244,0.880751
|
||||
245,0.880751
|
||||
247,0.874564
|
||||
248,0.874564
|
||||
249,0.874564
|
||||
250,0.714286
|
||||
253,0.934754
|
||||
254,0.934754
|
||||
255,0.938033
|
||||
256,0.938033
|
||||
257,0.938033
|
||||
258,0.938033
|
||||
259,0.941311
|
||||
260,0.941311
|
||||
261,0.941311
|
||||
262,0.941311
|
||||
263,0.938033
|
||||
264,0.934754
|
||||
265,0.934754
|
||||
266,0.934754
|
||||
267,0.934754
|
||||
268,0.934754
|
||||
269,0.934754
|
||||
270,0.934754
|
||||
271,0.975820
|
||||
272,0.983607
|
||||
273,0.990164
|
||||
274,0.990164
|
||||
275,0.990164
|
||||
277,0.990164
|
||||
278,0.990164
|
||||
279,0.990164
|
||||
280,0.990164
|
||||
281,0.990164
|
||||
282,0.990164
|
||||
283,0.990164
|
||||
284,0.990164
|
||||
285,0.990164
|
||||
286,0.928315
|
||||
287,0.931388
|
||||
288,0.961396
|
||||
289,0.930927
|
||||
290,0.930927
|
||||
291,0.930927
|
||||
292,0.993443
|
||||
293,0.993443
|
||||
294,0.993443
|
||||
295,0.993443
|
||||
296,0.993443
|
||||
297,0.993443
|
||||
298,0.993443
|
||||
299,0.993443
|
||||
300,0.993443
|
||||
301,0.993443
|
||||
302,0.996721
|
||||
303,1.000000
|
||||
304,1.000000
|
||||
305,1.000000
|
||||
306,1.000000
|
||||
307,1.000000
|
||||
308,1.000000
|
||||
309,1.000000
|
||||
310,1.000000
|
||||
311,1.000000
|
||||
312,1.000000
|
||||
313,1.000000
|
||||
314,1.000000
|
||||
315,1.000000
|
||||
316,1.000000
|
||||
317,1.000000
|
||||
318,0.967213
|
||||
319,0.936013
|
||||
320,0.936013
|
||||
321,0.936013
|
||||
322,0.967213
|
||||
323,0.967213
|
||||
324,0.967213
|
||||
325,0.967213
|
||||
326,0.944945
|
||||
327,0.894737
|
||||
328,0.967213
|
||||
329,0.967213
|
||||
330,0.967213
|
||||
331,0.967213
|
||||
332,0.967213
|
||||
333,0.966667
|
||||
334,0.966667
|
||||
335,0.966667
|
||||
336,0.966102
|
||||
337,0.966102
|
||||
338,0.966102
|
||||
339,0.965517
|
||||
340,1.000000
|
||||
341,1.000000
|
||||
342,1.000000
|
||||
343,1.000000
|
||||
344,1.000000
|
||||
345,1.000000
|
||||
346,1.000000
|
||||
347,0.990323
|
||||
348,1.000000
|
||||
349,1.000000
|
||||
350,0.951111
|
||||
351,1.000000
|
||||
|
File diff suppressed because it is too large
Load Diff
@ -1,66 +0,0 @@
|
||||
#ROW_NUMBER #RES_PAIR_SEQUENCE_SCORE
|
||||
1 0.972665
|
||||
2 0.972354
|
||||
3 0.973047
|
||||
4 0.971883
|
||||
5 0.972259
|
||||
6 0.973419
|
||||
7 0.973419
|
||||
8 0.973315
|
||||
9 0.973365
|
||||
10 0.972038
|
||||
11 0.971994
|
||||
12 0.971994
|
||||
13 0.967681
|
||||
14 0.971994
|
||||
15 0.974957
|
||||
16 0.972037
|
||||
17 0.972951
|
||||
18 0.972194
|
||||
19 0.972446
|
||||
20 0.972026
|
||||
21 0.972029
|
||||
22 0.972029
|
||||
23 0.972029
|
||||
24 0.971957
|
||||
25 0.971957
|
||||
26 0.617739
|
||||
27 0.972841
|
||||
28 0.963693
|
||||
29 0.972556
|
||||
30 0.971425
|
||||
31 0.985244
|
||||
32 0.975988
|
||||
33 0.970810
|
||||
34 0.959558
|
||||
35 0.973280
|
||||
36 0.973217
|
||||
37 0.973217
|
||||
38 0.970410
|
||||
39 0.972243
|
||||
40 0.969683
|
||||
41 0.523179
|
||||
42 0.971567
|
||||
43 0.972529
|
||||
44 0.975371
|
||||
45 0.975130
|
||||
46 0.972646
|
||||
47 0.972568
|
||||
48 0.973136
|
||||
49 0.974294
|
||||
50 0.964843
|
||||
51 0.965645
|
||||
52 0.965526
|
||||
53 0.964671
|
||||
54 0.901158
|
||||
55 0.894595
|
||||
56 0.894595
|
||||
57 0.834473
|
||||
58 0.822077
|
||||
59 0.818130
|
||||
60 0.964955
|
||||
61 0.378007
|
||||
62 0.964717
|
||||
63 0.972129
|
||||
64 0.592674
|
||||
#END
|
||||
@ -1,66 +0,0 @@
|
||||
SEQUENCE_NAME SEQUENCE_SCORE
|
||||
Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554 0.972665
|
||||
Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554 0.972354
|
||||
Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554 0.973047
|
||||
Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554 0.971883
|
||||
Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554 0.972259
|
||||
Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554 0.973419
|
||||
Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554 0.973419
|
||||
Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554 0.973315
|
||||
Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554 0.973365
|
||||
Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554 0.972038
|
||||
Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554 0.971994
|
||||
Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554 0.971994
|
||||
Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554 0.967681
|
||||
Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554 0.971994
|
||||
Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554 0.974957
|
||||
Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554 0.972037
|
||||
Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554 0.972951
|
||||
Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554 0.972194
|
||||
Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554 0.972446
|
||||
Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554 0.972026
|
||||
Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554 0.972029
|
||||
Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554 0.972029
|
||||
Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554 0.972029
|
||||
Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554 0.971957
|
||||
Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554 0.971957
|
||||
Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554 0.617739
|
||||
Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554 0.972841
|
||||
Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554 0.963693
|
||||
Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554 0.972556
|
||||
Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554 0.971425
|
||||
Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554 0.985244
|
||||
Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554 0.975988
|
||||
Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554 0.970810
|
||||
Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554 0.959558
|
||||
Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554 0.973280
|
||||
Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554 0.973217
|
||||
Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554 0.973217
|
||||
Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554 0.970410
|
||||
Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554 0.972243
|
||||
Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554 0.969683
|
||||
Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554 0.523179
|
||||
Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554 0.971567
|
||||
Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554 0.972529
|
||||
Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554 0.975371
|
||||
Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554 0.975130
|
||||
Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554 0.972646
|
||||
Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554 0.972568
|
||||
Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554 0.973136
|
||||
Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554 0.974294
|
||||
Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554 0.964843
|
||||
Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554 0.965645
|
||||
Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554 0.965526
|
||||
Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554 0.964671
|
||||
Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554 0.901158
|
||||
Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554 0.894595
|
||||
Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554 0.894595
|
||||
Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554 0.834473
|
||||
Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554 0.822077
|
||||
Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554 0.818130
|
||||
Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554 0.964955
|
||||
Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554 0.378007
|
||||
Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554 0.964717
|
||||
Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554 0.972129
|
||||
Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554 0.592674
|
||||
#END
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -1,128 +0,0 @@
|
||||
>seq0000
|
||||
-------------------------------------------------------------------------------------------------------------ISFDASVFKWGELAAHMKVVDGFADEMIAKCR-----YDLLSKFI-ISTRELRDILLNFIIAGRDTTAQLLSWCSYELCRNP----EIQSKIYDELK----TYQTVKMKYLEAVLYESLRLHPSVPNMTRFATRDI-QLN---NTIRKGDAVLVSNYVLGRLQKWW-DNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKHVAMMEAKIGLATILKDYR-MELKPGPMKNGCYINFIDRLSE--
|
||||
>seq0001
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLTKFI-ISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNP----EIQDKVYEELS----TYQSVKMKYLEAVLYEALRLHPSVPNMSRFATRDI-QLS---DVIRKGDCILVSNYVLGRLHQWW-ENALQFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYR-MELKPGPMKNGCFINFIDRSTK--
|
||||
>seq0002
|
||||
-----------------IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
|
||||
>seq0003
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVNLIPR-----
|
||||
>seq0004
|
||||
-------------------------------------------------------------------------------------------------------------ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
|
||||
>seq0005
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
|
||||
>seq0006
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
|
||||
>seq0007
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPR-----
|
||||
>seq0008
|
||||
PYFG--HHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTLKAHVKVINEFAERIIRSKRKDY--YDIMSLFL-ISDQELRDMALNFIIAGRDTTAQLLSWFSYAMTENA----DVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDI-DLP---ETIRKGNGIVIPTFAMGRMPWIW-KDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEAKIAVVKLFTKYK-LVPMPSVMKNGFKVKLIPRE----
|
||||
>seq0009
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LMSWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
|
||||
>seq0010
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-ISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
|
||||
>seq0011
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
|
||||
>seq0012
|
||||
-----------------------------------------------------------------------------------------------------------------------RS----------------SSKKQHF--YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LDALPSVMKNGFKVRLVPRCK---
|
||||
>seq0013
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
|
||||
>seq0014
|
||||
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDI-PLP---DVIRKGDGVIVPMYAMGRMPWLW-KNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFK-LEALPTVMKNGFKVKLIPRCK---
|
||||
>seq0015
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-ITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNK----QIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDI-KLP---DIIRKGDGIVIPTYAMGRMPWIW-NDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LQPLPSIMRNGFKVKLIPRDSK--
|
||||
>seq0016
|
||||
PLIG--HNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSLKKHSHILNDFAKKVIDDRKS----YDLLSLFL-VNVSELRDVCINFIVAGRDTTAQLLSWFMYELS-NP----KIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDI-ELPG--HIIRKGDGIVIPTYAMGRMPWIW-KDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKIAIVKLFKKYK-LVKLPSVMKYGYKVKLEPRNQ---
|
||||
>seq0017
|
||||
-----------------------------------------------------------------FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKHLKIINEFASNIIHKKRQQF--YDLISLFM-ITDEELRDIALNFIIAGRDTTAQLLSWFSYLVTENE----SVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDI-KLP---HIIRKGDGIVIPTFAMGRMPWIW-SNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIAIIKLFKKYK-LEAVPSVMKYGFNVKLVPRKQET-
|
||||
>seq0018
|
||||
---------------------------------------------------------------------------------------NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERK-----FDLLSLFL-TSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQ----ECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRFAKVDI-LLP---HVIRKGDGIVVPTYAMGRMPSLW-KDPLKFDPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFK-LEPLSSIMKNGFRVKLVPR-----
|
||||
>seq0019
|
||||
--------------------------KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQY--KDLLTLYF-ATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHA----HVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRFALVDI-KLP---HVIRKGDGVVVPVYAMGRMPWLW-PKPLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYR-IVARESIMKDGFYARLQPRAQQQQ
|
||||
>seq0020
|
||||
---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>seq0021
|
||||
---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>seq0022
|
||||
---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>seq0023
|
||||
-------------------------------------------------------------MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>seq0024
|
||||
-------------------------------------------------------------MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>seq0025
|
||||
PFFG--HNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
||||
>seq0026
|
||||
PFFG--HNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWRELHIHTAIIEQQISEVIQRNVN----YDLLSLFL-ASENELRDVAMNFIIAGRDTTAQLLSWFSYLLT-NP----KVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDI-PLL---NIIRKGDCIIIPTYAMGRMPWLW-NNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIVIIKLLRKYR-IVAIPSVMKNGFKVRLELR-----
|
||||
>seq0027
|
||||
-------------------------------------------------------------------------------------------------------------------------------------------------------------------ITMNFIIAGKDTTAQLLSWFFYVITHNR--SDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRFAKSDIFRVD---YTIRKGDGIVIPLYAMGRMPWIW-ENPDEFDPLRFQFLPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYR-FVTQESPMKNGYKVKLIPK-----
|
||||
>seq0028
|
||||
--------------------------LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERL--CDLLSLFI-ITDVELRDITINFVIAGRDTTAQLLSWFSYLIT-WP----QVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVREAKVDI-HLP---HIIRKGDGVIVPTYAMGRLPWLW-EKPEEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYK-FEPLPSAMKNGFKVKLVPRDTQ--
|
||||
>seq0029
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------LRDVAMNFIIAGRDTTAQLLSWFMYLFT-NK----EIEKPILNEINSII-NYIDVKLKYLENCFFETLRLRPAVPHLLRFAKTDI-QLK---YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
|
||||
>seq0030
|
||||
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
|
||||
>seq0031
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IKLNYLENSFLETLRLRPSVPHLVRKAVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQT---
|
||||
>seq0032
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NQ----HVEDKIMDEINQHI-NYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQTQF-
|
||||
>seq0033
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------RVRAAQLLSWFLYEITENN----EILSNINNEINEYI-NYDNIKLVYLENCFLETLRLRPSVPHLVRQANVDI-NIP---YTIRKDDTIIVPTYAMGRMDYIW-ENPLKFDPNRFKHSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFQKYK-FEPIKSVMKNGFKVKVVPNIFK--
|
||||
>seq0034
|
||||
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDI-PIP---YTIRKDDTIIVPTYAMGRMDYIW-ENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYK-FEPIKSVMKNGFKVKVVPIE----
|
||||
>seq0035
|
||||
PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLLSWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
|
||||
>seq0036
|
||||
PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLLSWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
|
||||
>seq0037
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------KQVQ--YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTLSWFTYELC--P----HVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDF-RLP---HIIRKGDGIVCAAYLMGHISHLW-DDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFK-IIPVPAPMKNGFKVTLHNIETD--
|
||||
>seq0038
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTLSWFIYELS--P----HVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRFATRDF-RIP---HIIRKGDGIVCAAYIMGHVPELW-NNPHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFK-IIPVPAPMKNGFKVTLECRN----
|
||||
>seq0039
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------IR--YDLLSLFL-ITEKELRDIAMNFIIAGRDTTAQTLSWFIYELT-SP----DVEENILKEIDS-IGTYENIKFKYLENALLETLRMHPAVPHLVRYATRDI-LLR---NIVRKGDGIVVGAYVMGHIPWLW-PDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYR-IEAIKAPMRYGFKVKLHPRL----
|
||||
>seq0040
|
||||
PFIGHIKNFIFIVDPKIIDLLFD--KRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYMFKSFCSTTDEFINKLS-----VDIYDMYNRLTLEAFTYVAFGTNLGAIS-------------------------------------------------------------------------------------------------------------------------QAPEELEFTSFDK-ICK------------------------------------RF-FDP---------------------------IKM------------------------------
|
||||
>seq0041
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG-------------
|
||||
>seq0042
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
|
||||
>seq0043
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
|
||||
>seq0044
|
||||
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDI-KLP---YTVRPGDEVFVSAYAMGRMPWVW-EDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK------
|
||||
>seq0045
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------FDLISMFI-ITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHK----LQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDI-ATH---YVIRKGDEVMVAAYSMARMPWLW-DDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR-----
|
||||
>seq0046
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------INFIIAGKDTTAQMLSWFFYHINN----LYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRTAVKDI-RTP---YVIRKGDEIFISAWSMGRAPWIW-DEPLQFKPERFMIDPSRFPAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE-----
|
||||
>seq0047
|
||||
PFVG--HHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEMRSHIDWIEDYIYKVIANRRAYY--YDLLSMFL-ISDKELRDITVNFIIAGKDTTAQMLSWFTYHLHK----LIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDI-ETY---YTIRAGDEVLICPLSMSRLEWIW-PNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP--
|
||||
>seq0048
|
||||
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
|
||||
>seq0049
|
||||
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------IAGRDTTSQMLSWFMFHLTKND-GMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
|
||||
>seq0050
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSD--MKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDI-QTP---YTIRKNDEIMISTYSIGRSKYIW-KDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE-------
|
||||
>seq0051
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQND-GMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK-------
|
||||
>seq0052
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MLSWFYFHLTQND-GMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRTAVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DDPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK-------
|
||||
>seq0053
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------VECKYIECCLKETLRLYPSVPHFSREMVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-ENADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM----------------
|
||||
>seq0054
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-GNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH-------
|
||||
>seq0055
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDF-KLKI--YTFYKGDEIVVTTFAMGRLPWLW-KNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE-------
|
||||
>seq0056
|
||||
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQMVTDL-TLNI--YTFEKGDEIVVFTIALGKLPWLW-ENADEFIPERFIYDAEIWPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD-------
|
||||
>seq0057
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSIFI-INDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDL-TLNI--YTFHKGDEVIVCTIALGKLPWLW-ENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK-------
|
||||
>seq0058
|
||||
------------------------------------------------------------------------------------------------------------------------------------------------------------------DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVREMVTDM-KINI--YIFEKGNEIIICTIALGKLPWLW-DNANEFIPERFIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP-------------------
|
||||
>seq0059
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LLSWFLYLVYENG--KKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERTAVEDI-KLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAPRICLGKHVALLEAKLVVIKLLRHFT-IQPVKSAMKNGYKIILKRR-----
|
||||
>seq0060
|
||||
------QNVVFISDPVQTKYIYD--RRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFETCSKRLVNKLP-----IDLFDMFNRLTMDGFVASAFGVYSDTIE-------------------------------------------------------------------------------------------------------------------------QAPHDTRFEAFDG-GCD------------------------------------RFIARP--------------------------FLETLKHAKRFCSIRERIESGE------------
|
||||
>seq0061
|
||||
-------------------------------------------------------------------------------------------------------------------------------------------ERIES--HDLLSLFM-FTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNP----HVLQLVIDEINTL--TYDNVELTYLESALLETQRLHPSVPTLNRQAKRDI-KLP---FTVKKGDIYMVHNYAMGRAPWIW-EDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME--------------------------------------
|
||||
>seq0062
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHP----DIVDQIRNEINQV--TYESLEMKYTESALLETQRLHPSVPSLIRFAFQDI-VLP---YTIRKGDAVNVFNYAMGRSPWIW-ENPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFN-FKAVPAPLKNGFQVHLQPLHPTQN
|
||||
>seq0063
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------DLLTLYA-ITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNP----HCLQQLKDEIRSI--SFKTLDMTYTESCILEAQRIYPSVPSLTRVAVTDI-PLP---YVIHKDEIVVISTFAMNRSPKIW-ENPLQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFD-FQIDMAPLTNGLPMRIIPLSSSV-
|
||||
@ -1,128 +0,0 @@
|
||||
>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554
|
||||
-------------------------------------------------------------------------------------------------------------ISFDASVFKWGELAAHMKVVDGFADEMIAKCR-----YDLLSKFI-ISTRELRDILLNFIIAGRDTTAQLLSWCSYELCRNP----EIQSKIYDELK----TYQTVKMKYLEAVLYESLRLHPSVPNMTRFATRDI-QLN---NTIRKGDAVLVSNYVLGRLQKWW-DNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKHVAMMEAKIGLATILKDYR-MELKPGPMKNGCYINFIDRLSE--
|
||||
>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLTKFI-ISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNP----EIQDKVYEELS----TYQSVKMKYLEAVLYEALRLHPSVPNMSRFATRDI-QLS---DVIRKGDCILVSNYVLGRLHQWW-ENALQFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYR-MELKPGPMKNGCFINFIDRSTK--
|
||||
>Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554
|
||||
-----------------IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
|
||||
>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVNLIPR-----
|
||||
>Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554
|
||||
-------------------------------------------------------------------------------------------------------------ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
|
||||
>Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
|
||||
>Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
|
||||
>Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPR-----
|
||||
>Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554
|
||||
PYFG--HHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTLKAHVKVINEFAERIIRSKRKDY--YDIMSLFL-ISDQELRDMALNFIIAGRDTTAQLLSWFSYAMTENA----DVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDI-DLP---ETIRKGNGIVIPTFAMGRMPWIW-KDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEAKIAVVKLFTKYK-LVPMPSVMKNGFKVKLIPRE----
|
||||
>Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LMSWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
|
||||
>Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-ISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
|
||||
>Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
|
||||
>Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554
|
||||
-----------------------------------------------------------------------------------------------------------------------RS----------------SSKKQHF--YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LDALPSVMKNGFKVRLVPRCK---
|
||||
>Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
|
||||
>Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554
|
||||
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDI-PLP---DVIRKGDGVIVPMYAMGRMPWLW-KNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFK-LEALPTVMKNGFKVKLIPRCK---
|
||||
>Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLMSLFL-ITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNK----QIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDI-KLP---DIIRKGDGIVIPTYAMGRMPWIW-NDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYK-LQPLPSIMRNGFKVKLIPRDSK--
|
||||
>Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554
|
||||
PLIG--HNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSLKKHSHILNDFAKKVIDDRKS----YDLLSLFL-VNVSELRDVCINFIVAGRDTTAQLLSWFMYELS-NP----KIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDI-ELPG--HIIRKGDGIVIPTYAMGRMPWIW-KDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKIAIVKLFKKYK-LVKLPSVMKYGYKVKLEPRNQ---
|
||||
>Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554
|
||||
-----------------------------------------------------------------FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKHLKIINEFASNIIHKKRQQF--YDLISLFM-ITDEELRDIALNFIIAGRDTTAQLLSWFSYLVTENE----SVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDI-KLP---HIIRKGDGIVIPTFAMGRMPWIW-SNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIAIIKLFKKYK-LEAVPSVMKYGFNVKLVPRKQET-
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554
|
||||
---------------------------------------------------------------------------------------NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERK-----FDLLSLFL-TSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQ----ECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRFAKVDI-LLP---HVIRKGDGIVVPTYAMGRMPSLW-KDPLKFDPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFK-LEPLSSIMKNGFRVKLVPR-----
|
||||
>Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554
|
||||
--------------------------KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQY--KDLLTLYF-ATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHA----HVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRFALVDI-KLP---HVIRKGDGVVVPVYAMGRMPWLW-PKPLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYR-IVARESIMKDGFYARLQPRAQQQQ
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554
|
||||
---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554
|
||||
---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554
|
||||
---------------------------------------------------MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554
|
||||
-------------------------------------------------------------MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554
|
||||
-------------------------------------------------------------MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554
|
||||
PFFG--HNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
||||
>Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554
|
||||
PFFG--HNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWRELHIHTAIIEQQISEVIQRNVN----YDLLSLFL-ASENELRDVAMNFIIAGRDTTAQLLSWFSYLLT-NP----KVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDI-PLL---NIIRKGDCIIIPTYAMGRMPWLW-NNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIVIIKLLRKYR-IVAIPSVMKNGFKVRLELR-----
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554
|
||||
-------------------------------------------------------------------------------------------------------------------------------------------------------------------ITMNFIIAGKDTTAQLLSWFFYVITHNR--SDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRFAKSDIFRVD---YTIRKGDGIVIPLYAMGRMPWIW-ENPDEFDPLRFQFLPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYR-FVTQESPMKNGYKVKLIPK-----
|
||||
>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554
|
||||
--------------------------LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERL--CDLLSLFI-ITDVELRDITINFVIAGRDTTAQLLSWFSYLIT-WP----QVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVREAKVDI-HLP---HIIRKGDGVIVPTYAMGRLPWLW-EKPEEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYK-FEPLPSAMKNGFKVKLVPRDTQ--
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------LRDVAMNFIIAGRDTTAQLLSWFMYLFT-NK----EIEKPILNEINSII-NYIDVKLKYLENCFFETLRLRPAVPHLLRFAKTDI-QLK---YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554
|
||||
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IKLNYLENSFLETLRLRPSVPHLVRKAVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQT---
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NQ----HVEDKIMDEINQHI-NYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQTQF-
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------RVRAAQLLSWFLYEITENN----EILSNINNEINEYI-NYDNIKLVYLENCFLETLRLRPSVPHLVRQANVDI-NIP---YTIRKDDTIIVPTYAMGRMDYIW-ENPLKFDPNRFKHSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFQKYK-FEPIKSVMKNGFKVKVVPNIFK--
|
||||
>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554
|
||||
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDI-PIP---YTIRKDDTIIVPTYAMGRMDYIW-ENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYK-FEPIKSVMKNGFKVKVVPIE----
|
||||
>Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554
|
||||
PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLLSWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
|
||||
>Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554
|
||||
PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLLSWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------KQVQ--YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTLSWFTYELC--P----HVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDF-RLP---HIIRKGDGIVCAAYLMGHISHLW-DDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFK-IIPVPAPMKNGFKVTLHNIETD--
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTLSWFIYELS--P----HVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRFATRDF-RIP---HIIRKGDGIVCAAYIMGHVPELW-NNPHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFK-IIPVPAPMKNGFKVTLECRN----
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------IR--YDLLSLFL-ITEKELRDIAMNFIIAGRDTTAQTLSWFIYELT-SP----DVEENILKEIDS-IGTYENIKFKYLENALLETLRMHPAVPHLVRYATRDI-LLR---NIVRKGDGIVVGAYVMGHIPWLW-PDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYR-IEAIKAPMRYGFKVKLHPRL----
|
||||
>Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554
|
||||
PFIGHIKNFIFIVDPKIIDLLFD--KRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYMFKSFCSTTDEFINKLS-----VDIYDMYNRLTLEAFTYVAFGTNLGAIS-------------------------------------------------------------------------------------------------------------------------QAPEELEFTSFDK-ICK------------------------------------RF-FDP---------------------------IKM------------------------------
|
||||
>Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG-------------
|
||||
>Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
|
||||
>Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KVKCSFIECCLKESLRLYPSVPHLVRTAVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
|
||||
>Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554
|
||||
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDI-KLP---YTVRPGDEVFVSAYAMGRMPWVW-EDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK------
|
||||
>Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------FDLISMFI-ITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHK----LQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDI-ATH---YVIRKGDEVMVAAYSMARMPWLW-DDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR-----
|
||||
>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------------------------INFIIAGKDTTAQMLSWFFYHINN----LYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRTAVKDI-RTP---YVIRKGDEIFISAWSMGRAPWIW-DEPLQFKPERFMIDPSRFPAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE-----
|
||||
>Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554
|
||||
PFVG--HHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEMRSHIDWIEDYIYKVIANRRAYY--YDLLSMFL-ISDKELRDITVNFIIAGKDTTAQMLSWFTYHLHK----LIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDI-ETY---YTIRAGDEVLICPLSMSRLEWIW-PNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP--
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554
|
||||
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554
|
||||
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------IAGRDTTSQMLSWFMFHLTKND-GMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
|
||||
>Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSD--MKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDI-QTP---YTIRKNDEIMISTYSIGRSKYIW-KDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE-------
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSMFI-ISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQND-GMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK-------
|
||||
>Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MLSWFYFHLTQND-GMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRTAVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DDPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK-------
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------VECKYIECCLKETLRLYPSVPHFSREMVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-ENADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM----------------
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-GNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH-------
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDF-KLKI--YTFYKGDEIVVTTFAMGRLPWLW-KNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE-------
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554
|
||||
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQMVTDL-TLNI--YTFEKGDEIVVFTIALGKLPWLW-ENADEFIPERFIYDAEIWPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD-------
|
||||
>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YDLLSIFI-INDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDL-TLNI--YTFHKGDEVIVCTIALGKLPWLW-ENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK-------
|
||||
>Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554
|
||||
------------------------------------------------------------------------------------------------------------------------------------------------------------------DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVREMVTDM-KINI--YIFEKGNEIIICTIALGKLPWLW-DNANEFIPERFIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP-------------------
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554
|
||||
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LLSWFLYLVYENG--KKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERTAVEDI-KLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAPRICLGKHVALLEAKLVVIKLLRHFT-IQPVKSAMKNGYKIILKRR-----
|
||||
>Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554
|
||||
------QNVVFISDPVQTKYIYD--RRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFETCSKRLVNKLP-----IDLFDMFNRLTMDGFVASAFGVYSDTIE-------------------------------------------------------------------------------------------------------------------------QAPHDTRFEAFDG-GCD------------------------------------RFIARP--------------------------FLETLKHAKRFCSIRERIESGE------------
|
||||
>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554
|
||||
-------------------------------------------------------------------------------------------------------------------------------------------ERIES--HDLLSLFM-FTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNP----HVLQLVIDEINTL--TYDNVELTYLESALLETQRLHPSVPTLNRQAKRDI-KLP---FTVKKGDIYMVHNYAMGRAPWIW-EDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME--------------------------------------
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554
|
||||
--------------------------------------------------------------------------------------------------------------------------------------------------YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHP----DIVDQIRNEINQV--TYESLEMKYTESALLETQRLHPSVPSLIRFAFQDI-VLP---YTIRKGDAVNVFNYAMGRSPWIW-ENPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFN-FKAVPAPLKNGFQVHLQPLHPTQN
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554
|
||||
---------------------------------------------------------------------------------------------------------------------------------------------------DLLTLYA-ITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNP----HCLQQLKDEIRSI--SFKTLDMTYTESCILEAQRIYPSVPSLTRVAVTDI-PLP---YVIHKDEIVVISTFAMNRSPKIW-ENPLQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFD-FQIDMAPLTNGLPMRIIPLSSSV-
|
||||
@ -1,448 +0,0 @@
|
||||
>seq0000
|
||||
------------------------------------------------------------
|
||||
-------------------------------------------------ISFDASVFKWG
|
||||
ELAAHMKVVDGFADEMIAKCR-----YDLLSKFI-ISTRELRDILLNFIIAGRDTTAQLL
|
||||
SWCSYELCRNP----EIQSKIYDELK----TYQTVKMKYLEAVLYESLRLHPSVPNMTRF
|
||||
ATRDI-QLN---NTIRKGDAVLVSNYVLGRLQKWW-DNPYKFDPMRFYYKAHEYTNFNIP
|
||||
PRLCLGKHVAMMEAKIGLATILKDYR-MELKPGPMKNGCYINFIDRLSE--
|
||||
>seq0001
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLTKFI-ISTRELRDILLNFIIAGRDTTAQLL
|
||||
SWCSYELCLNP----EIQDKVYEELS----TYQSVKMKYLEAVLYEALRLHPSVPNMSRF
|
||||
ATRDI-QLS---DVIRKGDCILVSNYVLGRLHQWW-ENALQFDPMRFYYKAHEYTNFNVP
|
||||
PRLCLGKHVALMEAKIALATVLKDYR-MELKPGPMKNGCFINFIDRSTK--
|
||||
>seq0002
|
||||
-----------------IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRD
|
||||
YMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVR
|
||||
TLKKHEQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLL
|
||||
SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
|
||||
AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
|
||||
PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
|
||||
>seq0003
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------------LL
|
||||
SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
|
||||
AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
|
||||
PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVNLIPR-----
|
||||
>seq0004
|
||||
------------------------------------------------------------
|
||||
-------------------------------------------------ISFDDGQTRVR
|
||||
TLKKHVQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLL
|
||||
SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
|
||||
AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
|
||||
PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
|
||||
>seq0005
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
|
||||
YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
|
||||
TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
|
||||
SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
|
||||
AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
|
||||
>seq0006
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
|
||||
YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
|
||||
TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
|
||||
SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
|
||||
AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
|
||||
>seq0007
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
|
||||
YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
|
||||
TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
|
||||
SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
|
||||
AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPR-----
|
||||
>seq0008
|
||||
PYFG--HHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRD
|
||||
YMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKAR
|
||||
TLKAHVKVINEFAERIIRSKRKDY--YDIMSLFL-ISDQELRDMALNFIIAGRDTTAQLL
|
||||
SWFSYAMTENA----DVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRY
|
||||
AKVDI-DLP---ETIRKGNGIVIPTFAMGRMPWIW-KDPLKFDPDRFNYTASQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAVVKLFTKYK-LVPMPSVMKNGFKVKLIPRE----
|
||||
>seq0009
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------------LM
|
||||
SWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRY
|
||||
AKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIP
|
||||
PRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
|
||||
>seq0010
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLMSLFL-ISDDELRDVALNFILAGRDTTAQLM
|
||||
SWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRY
|
||||
AKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIP
|
||||
PRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
|
||||
>seq0011
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
|
||||
SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
|
||||
AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
|
||||
>seq0012
|
||||
------------------------------------------------------------
|
||||
-----------------------------------------------------------R
|
||||
S----------------SSKKQHF--YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
|
||||
SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
|
||||
AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LDALPSVMKNGFKVRLVPRCK---
|
||||
>seq0013
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
|
||||
SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
|
||||
AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
|
||||
>seq0014
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRY
|
||||
AKVDI-PLP---DVIRKGDGVIVPMYAMGRMPWLW-KNPDKFDPERFNYTPAEYPAFNIP
|
||||
PRVCLGKHVALMEAKIAVIKLLKKFK-LEALPTVMKNGFKVKLIPRCK---
|
||||
>seq0015
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLMSLFL-ITDDELRDIALNFIIAGRDTTAQLL
|
||||
SWFSYCITDNK----QIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRY
|
||||
AKIDI-KLP---DIIRKGDGIVIPTYAMGRMPWIW-NDPLKFNPDRFNYSPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LQPLPSIMRNGFKVKLIPRDSK--
|
||||
>seq0016
|
||||
PLIG--HNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRD
|
||||
YMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLK
|
||||
SLKKHSHILNDFAKKVIDDRKS----YDLLSLFL-VNVSELRDVCINFIVAGRDTTAQLL
|
||||
SWFMYELS-NP----KIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRY
|
||||
AKCDI-ELPG--HIIRKGDGIVIPTYAMGRMPWIW-KDPLKFNPDRFKHPPSKYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIVKLFKKYK-LVKLPSVMKYGYKVKLEPRNQ---
|
||||
>seq0017
|
||||
------------------------------------------------------------
|
||||
-----FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWR
|
||||
TLKKHLKIINEFASNIIHKKRQQF--YDLISLFM-ITDEELRDIALNFIIAGRDTTAQLL
|
||||
SWFSYLVTENE----SVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRY
|
||||
AKTDI-KLP---HIIRKGDGIVIPTFAMGRMPWIW-SNPLEFNPDRFKFTPAEYPAFNLP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEAVPSVMKYGFNVKLVPRKQET-
|
||||
>seq0018
|
||||
------------------------------------------------------------
|
||||
---------------------------NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLR
|
||||
ELRKHLKVVNEFVSKVIVERK-----FDLLSLFL-TSDKELRDVAMNFIVAGRDTTAQLL
|
||||
SWFSYLISENQ----ECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRF
|
||||
AKVDI-LLP---HVIRKGDGIVVPTYAMGRMPSLW-KDPLKFDPSRFEYTPSEYPAFNIP
|
||||
PRLCLGKHVALLESKIAIIRLFRKFK-LEPLSSIMKNGFRVKLVPR-----
|
||||
>seq0019
|
||||
--------------------------KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRD
|
||||
FMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFK
|
||||
ELKKHAGILNDKIGLLVRQRKEQY--KDLLTLYF-ATDLELRDLIMNFVVAGRDTTAQLC
|
||||
SWFSYEISEHA----HVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRF
|
||||
ALVDI-KLP---HVIRKGDGVVVPVYAMGRMPWLW-PKPLVFDPMRFEYTPALFPAFNIP
|
||||
PRLCLGKHLALLEAKVVMVKILRKYR-IVARESIMKDGFYARLQPRAQQQQ
|
||||
>seq0020
|
||||
---------------------------------------------------MFTVRALRD
|
||||
YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
|
||||
ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
|
||||
SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
|
||||
AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
|
||||
PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>seq0021
|
||||
---------------------------------------------------MFTVRALRD
|
||||
YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
|
||||
ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
|
||||
SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
|
||||
AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
|
||||
PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>seq0022
|
||||
---------------------------------------------------MFTVRALRD
|
||||
YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
|
||||
ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
|
||||
SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
|
||||
AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
|
||||
PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>seq0023
|
||||
------------------------------------------------------------
|
||||
-MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
|
||||
ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
|
||||
SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
|
||||
AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
|
||||
PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>seq0024
|
||||
------------------------------------------------------------
|
||||
-MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
|
||||
ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
|
||||
SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
|
||||
AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
|
||||
PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>seq0025
|
||||
PFFG--HNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRD
|
||||
YMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ----
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
---------------------------------------------------
|
||||
>seq0026
|
||||
PFFG--HNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLRE
|
||||
YMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWR
|
||||
ELHIHTAIIEQQISEVIQRNVN----YDLLSLFL-ASENELRDVAMNFIIAGRDTTAQLL
|
||||
SWFSYLLT-NP----KVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRY
|
||||
AKTDI-PLL---NIIRKGDCIIIPTYAMGRMPWLW-NNALTFDPSRFEYSPAQYPAFNIP
|
||||
PRLCLGKHVALLEAKIVIIKLLRKYR-IVAIPSVMKNGFKVRLELR-----
|
||||
>seq0027
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
-------------------------------------------ITMNFIIAGKDTTAQLL
|
||||
SWFFYVITHNR--SDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRF
|
||||
AKSDIFRVD---YTIRKGDGIVIPLYAMGRMPWIW-ENPDEFDPLRFQFLPSEYPAFNIP
|
||||
PRLCLGKHVALMEAKIAVIKLLKKYR-FVTQESPMKNGYKVKLIPK-----
|
||||
>seq0028
|
||||
--------------------------LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRD
|
||||
YMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFK
|
||||
ELLFHEKTINNMVWDLVHKCKERL--CDLLSLFI-ITDVELRDITINFVIAGRDTTAQLL
|
||||
SWFSYLIT-WP----QVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVRE
|
||||
AKVDI-HLP---HIIRKGDGVIVPTYAMGRLPWLW-EKPEEMNPDRFQFTPSEYPAFNIP
|
||||
PRLCLGKHVSLMEAKIQIVKLLPKYK-FEPLPSAMKNGFKVKLVPRDTQ--
|
||||
>seq0029
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------LRDVAMNFIIAGRDTTAQLL
|
||||
SWFMYLFT-NK----EIEKPILNEINSII-NYIDVKLKYLENCFFETLRLRPAVPHLLRF
|
||||
AKTDI-QLK---YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIP
|
||||
PRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
|
||||
>seq0030
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIP
|
||||
PRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
|
||||
>seq0031
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------IKLNYLENSFLETLRLRPSVPHLVRK
|
||||
AVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIK
|
||||
PRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQT---
|
||||
>seq0032
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
---------NQ----HVEDKIMDEINQHI-NYNTIKLNYLENSFLETLRLRPSVPHLVRK
|
||||
AVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIK
|
||||
PRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQTQF-
|
||||
>seq0033
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------RVRAAQLL
|
||||
SWFLYEITENN----EILSNINNEINEYI-NYDNIKLVYLENCFLETLRLRPSVPHLVRQ
|
||||
ANVDI-NIP---YTIRKDDTIIVPTYAMGRMDYIW-ENPLKFDPNRFKHSPSKYPAFNIK
|
||||
PRLCLGKHVALLEAKIAIAKLFQKYK-FEPIKSVMKNGFKVKVVPNIFK--
|
||||
>seq0034
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
-----------------------SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQ
|
||||
ANVDI-PIP---YTIRKDDTIIVPTYAMGRMDYIW-ENALTFDPNRFKYSPSKYPAFNIK
|
||||
PRLCLGKHVALLEAKIAIAKLFKKYK-FEPIKSVMKNGFKVKVVPIE----
|
||||
>seq0035
|
||||
PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKD
|
||||
YMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYG
|
||||
ELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLL
|
||||
SWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRV
|
||||
AKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIP
|
||||
PRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
|
||||
>seq0036
|
||||
PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKD
|
||||
YMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYG
|
||||
ELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLL
|
||||
SWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRV
|
||||
AKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIP
|
||||
PRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
|
||||
>seq0037
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------KQVQ--YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTL
|
||||
SWFTYELC--P----HVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRF
|
||||
ATRDF-RLP---HIIRKGDGIVCAAYLMGHISHLW-DDPERFDPTRFEYDPSYFPAFNIA
|
||||
PRICLGKHVALLEAKIAAIKLFKKFK-IIPVPAPMKNGFKVTLHNIETD--
|
||||
>seq0038
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTL
|
||||
SWFIYELS--P----HVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRF
|
||||
ATRDF-RIP---HIIRKGDGIVCAAYIMGHVPELW-NNPHQFDPTRFEYDPSYFPAFNIA
|
||||
PRLCLGKHVALLEAKIAAVKLLKKFK-IIPVPAPMKNGFKVTLECRN----
|
||||
>seq0039
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------IR--YDLLSLFL-ITEKELRDIAMNFIIAGRDTTAQTL
|
||||
SWFIYELT-SP----DVEENILKEIDS-IGTYENIKFKYLENALLETLRMHPAVPHLVRY
|
||||
ATRDI-LLR---NIVRKGDGIVVGAYVMGHIPWLW-PDPERFDPTRFEYDPCYFPVFNVA
|
||||
PRLCLGKHVALLEAKIAAVKLLKKYR-IEAIKAPMRYGFKVKLHPRL----
|
||||
>seq0040
|
||||
PFIGHIKNFIFIVDPKIIDLLFD--KRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRD
|
||||
YMFKSFCSTTDEFINKLS-----VDIYDMYNRLTLEAFTYVAFGTNLGAIS---------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------QAPEELEF
|
||||
TSFDK-ICK------------------------------------RF-FDP---------
|
||||
------------------IKM------------------------------
|
||||
>seq0041
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQML
|
||||
SWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRT
|
||||
AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
|
||||
PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG-------------
|
||||
>seq0042
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQML
|
||||
SWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRT
|
||||
AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
|
||||
PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
|
||||
>seq0043
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
---------------------------------KVKCSFIECCLKESLRLYPSVPHLVRT
|
||||
AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
|
||||
PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
|
||||
>seq0044
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------EYEKVKCRYIECCLKESLRLYPSVPHLVRT
|
||||
AVKDI-KLP---YTVRPGDEVFVSAYAMGRMPWVW-EDPLEFKPERFQPDPSMYPAFNIA
|
||||
PRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK------
|
||||
>seq0045
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------FDLISMFI-ITDEELRDITFSFIIAGKDTTAQML
|
||||
SWLMYHLHK----LQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRT
|
||||
PVKDI-ATH---YVIRKGDEVMVAAYSMARMPWLW-DDPLAFKPERFMYDPSLYPAFNIA
|
||||
PRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR-----
|
||||
>seq0046
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
---------------------------------------------INFIIAGKDTTAQML
|
||||
SWFFYHINN----LYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRT
|
||||
AVKDI-RTP---YVIRKGDEIFISAWSMGRAPWIW-DEPLQFKPERFMIDPSRFPAFNVA
|
||||
PRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE-----
|
||||
>seq0047
|
||||
PFVG--HHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRD
|
||||
YMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKK
|
||||
EMRSHIDWIEDYIYKVIANRRAYY--YDLLSMFL-ISDKELRDITVNFIIAGKDTTAQML
|
||||
SWFTYHLHK----LIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARA
|
||||
AVVDI-ETY---YTIRAGDEVLICPLSMSRLEWIW-PNAEQFIPERFAFDPWVYPAFNIP
|
||||
PRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP--
|
||||
>seq0048
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRT
|
||||
AIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLK
|
||||
PRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
|
||||
>seq0049
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
-------------------------------------------------IAGRDTTSQML
|
||||
SWFMFHLTKND-GMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRT
|
||||
AIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLK
|
||||
PRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
|
||||
>seq0050
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSMFI-ISDRQLRDITMNFIIAGRDTTSQML
|
||||
SWFMYHLTNSD--MKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRT
|
||||
AIEDI-QTP---YTIRKNDEIMISTYSIGRSKYIW-KDPLTFNPERFLYDPSVYPAFNLK
|
||||
PRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE-------
|
||||
>seq0051
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSMFI-ISDDELRDITMNFIIAGRDTTSHML
|
||||
SWFLFHLTQND-GMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRT
|
||||
AVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DKPLKFDANRFIYDASVYPAFNIQ
|
||||
PRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK-------
|
||||
>seq0052
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------------ML
|
||||
SWFYFHLTQND-GMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRT
|
||||
AVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DDPLKFDANRFIYDASVYPAFNIQ
|
||||
PRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK-------
|
||||
>seq0053
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------VECKYIECCLKETLRLYPSVPHFSRE
|
||||
MVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-ENADKFIPERFMYDNSQYPAFNIA
|
||||
PRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM----------------
|
||||
>seq0054
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSRE
|
||||
MVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-GNADKFIPERFMYDNSQYPAFNIA
|
||||
PRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH-------
|
||||
>seq0055
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSRE
|
||||
MVKDF-KLKI--YTFYKGDEIVVTTFAMGRLPWLW-KNAEKFVPERFMYDQSKYVAFNIS
|
||||
PRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE-------
|
||||
>seq0056
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
-------------------------------------------------IAGRDTTSQMI
|
||||
SWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQ
|
||||
MVTDL-TLNI--YTFEKGDEIVVFTIALGKLPWLW-ENADEFIPERFIYDAEIWPAFNIA
|
||||
PRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD-------
|
||||
>seq0057
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSIFI-INDKFLRDVTMNFIIAGRDTTSQML
|
||||
SWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVRE
|
||||
MVSDL-TLNI--YTFHKGDEVIVCTIALGKLPWLW-ENANEFIPERFIYDAHIWPAFNIA
|
||||
PRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK-------
|
||||
>seq0058
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------DITMNFIIAGRDTTSQML
|
||||
SWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVRE
|
||||
MVTDM-KINI--YIFEKGNEIIICTIALGKLPWLW-DNANEFIPERFIYDNHIYPAFNIL
|
||||
PRTCLGKNVALLEGKIAIISMFSNFNKFKAVP-------------------
|
||||
>seq0059
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------------LL
|
||||
SWFLYLVYENG--KKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERT
|
||||
AVEDI-KLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIA
|
||||
PRICLGKHVALLEAKLVVIKLLRHFT-IQPVKSAMKNGYKIILKRR-----
|
||||
>seq0060
|
||||
------QNVVFISDPVQTKYIYD--RRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKH
|
||||
YMFENFETCSKRLVNKLP-----IDLFDMFNRLTMDGFVASAFGVYSDTIE---------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------QAPHDTRF
|
||||
EAFDG-GCD------------------------------------RFIARP---------
|
||||
-----------------FLETLKHAKRFCSIRERIESGE------------
|
||||
>seq0061
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
-------------------ERIES--HDLLSLFM-FTEEELQDLCLNFIIAGRDTTAENI
|
||||
SWLMYELSKNP----HVLQLVIDEINTL--TYDNVELTYLESALLETQRLHPSVPTLNRQ
|
||||
AKRDI-KLP---FTVKKGDIYMVHNYAMGRAPWIW-EDPLRFDPTRFSYEPQVFPQFNIA
|
||||
PRMCLGKHVAMME--------------------------------------
|
||||
>seq0062
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YNLLSLFLNYTLDELRDICINFIIAGRDTTAETL
|
||||
TWLCVELSSHP----DIVDQIRNEINQV--TYESLEMKYTESALLETQRLHPSVPSLIRF
|
||||
AFQDI-VLP---YTIRKGDAVNVFNYAMGRSPWIW-ENPLQFHPPRFQFHPSVYPAFNIG
|
||||
QRLCLGRHVALMHAKVVLYHLFKHFN-FKAVPAPLKNGFQVHLQPLHPTQN
|
||||
>seq0063
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
---------------------------DLLTLYA-ITRSELQDVCVNFIIAGRDTTALNL
|
||||
CWLFILLAQNP----HCLQQLKDEIRSI--SFKTLDMTYTESCILEAQRIYPSVPSLTRV
|
||||
AVTDI-PLP---YVIHKDEIVVISTFAMNRSPKIW-ENPLQFDPSRFEHEPHIYPSFNIG
|
||||
QRLCLGRHVALLVAKVVLYHFFQNFD-FQIDMAPLTNGLPMRIIPLSSSV-
|
||||
@ -1,448 +0,0 @@
|
||||
>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554
|
||||
------------------------------------------------------------
|
||||
-------------------------------------------------ISFDASVFKWG
|
||||
ELAAHMKVVDGFADEMIAKCR-----YDLLSKFI-ISTRELRDILLNFIIAGRDTTAQLL
|
||||
SWCSYELCRNP----EIQSKIYDELK----TYQTVKMKYLEAVLYESLRLHPSVPNMTRF
|
||||
ATRDI-QLN---NTIRKGDAVLVSNYVLGRLQKWW-DNPYKFDPMRFYYKAHEYTNFNIP
|
||||
PRLCLGKHVAMMEAKIGLATILKDYR-MELKPGPMKNGCYINFIDRLSE--
|
||||
>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLTKFI-ISTRELRDILLNFIIAGRDTTAQLL
|
||||
SWCSYELCLNP----EIQDKVYEELS----TYQSVKMKYLEAVLYEALRLHPSVPNMSRF
|
||||
ATRDI-QLS---DVIRKGDCILVSNYVLGRLHQWW-ENALQFDPMRFYYKAHEYTNFNVP
|
||||
PRLCLGKHVALMEAKIALATVLKDYR-MELKPGPMKNGCFINFIDRSTK--
|
||||
>Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554
|
||||
-----------------IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRD
|
||||
YMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVR
|
||||
TLKKHEQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLL
|
||||
SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
|
||||
AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
|
||||
PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
|
||||
>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------------LL
|
||||
SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
|
||||
AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
|
||||
PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVNLIPR-----
|
||||
>Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554
|
||||
------------------------------------------------------------
|
||||
-------------------------------------------------ISFDDGQTRVR
|
||||
TLKKHVQIINEFANTIIQKKRKHF--YDIMSLFL-VSDAELRDVALNFIVAGRDTTAQLL
|
||||
SWFSYAMSENK----GVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRY
|
||||
AKVDI-ELP---DVIRKGDAIIIPTFAMGRMPWIW-KDPLKFNPDRFNFTPSQYPAFNIP
|
||||
PRLCLGKHVALMEAKIAIIKLFKKYK-LEAVPSVMKYGFKVKLIPR-----
|
||||
>Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
|
||||
YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
|
||||
TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
|
||||
SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
|
||||
AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
|
||||
>Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
|
||||
YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
|
||||
TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
|
||||
SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
|
||||
AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPRES---
|
||||
>Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554
|
||||
PYFG--HNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRD
|
||||
YMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKAR
|
||||
TLKKHINIINEFANEFIQKKREHL--YDIMWLFL-ISDEELRDIALNFIIAGRDTTAQLL
|
||||
SWCTYLLSENQ----HVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRY
|
||||
AKVDI-ALP---DIIRKGDGIVVPTFAMGRMPWIW-KDPLKFNPDRFNYTPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEPVSSVMKNGFKVKLIPR-----
|
||||
>Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554
|
||||
PYFG--HHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRD
|
||||
YMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKAR
|
||||
TLKAHVKVINEFAERIIRSKRKDY--YDIMSLFL-ISDQELRDMALNFIIAGRDTTAQLL
|
||||
SWFSYAMTENA----DVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRY
|
||||
AKVDI-DLP---ETIRKGNGIVIPTFAMGRMPWIW-KDPLKFDPDRFNYTASQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAVVKLFTKYK-LVPMPSVMKNGFKVKLIPRE----
|
||||
>Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------------LM
|
||||
SWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRY
|
||||
AKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIP
|
||||
PRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
|
||||
>Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLMSLFL-ISDDELRDVALNFILAGRDTTAQLM
|
||||
SWFSYAMTENE----EVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRY
|
||||
AKVDI-ALP---HVIRKGDGLIVPSFAMGRMPWIW-KDPNTFNPDRFKYTPAQYPAFNIP
|
||||
PRLCLGKHVALLEAKIMIIKLFKKYK-LEAVPNIMKNGLKVRLIPRGK---
|
||||
>Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
|
||||
SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
|
||||
AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
|
||||
>Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554
|
||||
------------------------------------------------------------
|
||||
-----------------------------------------------------------R
|
||||
S----------------SSKKQHF--YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
|
||||
SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
|
||||
AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LDALPSVMKNGFKVRLVPRCK---
|
||||
>Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLMSLFL-VSDDELRDVALNFIIAGRDTTAQLL
|
||||
SWFSYAITENE----EVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRY
|
||||
AKVDI-TLP---DVVRKGDGIIIPTYAMGRMPWIW-KDPLKFDPDRFNYSPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEALPSVMKNGFKVRLVPRCK---
|
||||
>Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRY
|
||||
AKVDI-PLP---DVIRKGDGVIVPMYAMGRMPWLW-KNPDKFDPERFNYTPAEYPAFNIP
|
||||
PRVCLGKHVALMEAKIAVIKLLKKFK-LEALPTVMKNGFKVKLIPRCK---
|
||||
>Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLMSLFL-ITDDELRDIALNFIIAGRDTTAQLL
|
||||
SWFSYCITDNK----QIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRY
|
||||
AKIDI-KLP---DIIRKGDGIVIPTYAMGRMPWIW-NDPLKFNPDRFNYSPSQYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LQPLPSIMRNGFKVKLIPRDSK--
|
||||
>Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554
|
||||
PLIG--HNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRD
|
||||
YMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLK
|
||||
SLKKHSHILNDFAKKVIDDRKS----YDLLSLFL-VNVSELRDVCINFIVAGRDTTAQLL
|
||||
SWFMYELS-NP----KIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRY
|
||||
AKCDI-ELPG--HIIRKGDGIVIPTYAMGRMPWIW-KDPLKFNPDRFKHPPSKYPAFNIP
|
||||
PRLCLGKHVALLEAKIAIVKLFKKYK-LVKLPSVMKYGYKVKLEPRNQ---
|
||||
>Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554
|
||||
------------------------------------------------------------
|
||||
-----FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWR
|
||||
TLKKHLKIINEFASNIIHKKRQQF--YDLISLFM-ITDEELRDIALNFIIAGRDTTAQLL
|
||||
SWFSYLVTENE----SVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRY
|
||||
AKTDI-KLP---HIIRKGDGIVIPTFAMGRMPWIW-SNPLEFNPDRFKFTPAEYPAFNLP
|
||||
PRLCLGKHVALLEAKIAIIKLFKKYK-LEAVPSVMKYGFNVKLVPRKQET-
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554
|
||||
------------------------------------------------------------
|
||||
---------------------------NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLR
|
||||
ELRKHLKVVNEFVSKVIVERK-----FDLLSLFL-TSDKELRDVAMNFIVAGRDTTAQLL
|
||||
SWFSYLISENQ----ECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRF
|
||||
AKVDI-LLP---HVIRKGDGIVVPTYAMGRMPSLW-KDPLKFDPSRFEYTPSEYPAFNIP
|
||||
PRLCLGKHVALLESKIAIIRLFRKFK-LEPLSSIMKNGFRVKLVPR-----
|
||||
>Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554
|
||||
--------------------------KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRD
|
||||
FMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFK
|
||||
ELKKHAGILNDKIGLLVRQRKEQY--KDLLTLYF-ATDLELRDLIMNFVVAGRDTTAQLC
|
||||
SWFSYEISEHA----HVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRF
|
||||
ALVDI-KLP---HVIRKGDGVVVPVYAMGRMPWLW-PKPLVFDPMRFEYTPALFPAFNIP
|
||||
PRLCLGKHLALLEAKVVMVKILRKYR-IVARESIMKDGFYARLQPRAQQQQ
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554
|
||||
---------------------------------------------------MFTVRALRD
|
||||
YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
|
||||
ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
|
||||
SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
|
||||
AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
|
||||
PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554
|
||||
---------------------------------------------------MFTVRALRD
|
||||
YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
|
||||
ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
|
||||
SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
|
||||
AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
|
||||
PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554
|
||||
---------------------------------------------------MFTVRALRD
|
||||
YMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
|
||||
ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
|
||||
SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
|
||||
AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
|
||||
PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554
|
||||
------------------------------------------------------------
|
||||
-MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
|
||||
ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
|
||||
SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
|
||||
AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
|
||||
PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554
|
||||
------------------------------------------------------------
|
||||
-MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWR
|
||||
ELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFL-ASYKELKDVTMNFIMAGKDTTAQLL
|
||||
SWFSWSLT-NP----EVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRY
|
||||
AKVDI-PLP---HVIRKGDGIVVPTYAMGRMAWLW-PNPTKFDPTRFEFTPAVYPAFNLP
|
||||
PRVCLGKHVALLECKIVMIKLLRRFR-IVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554
|
||||
PFFG--HNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRD
|
||||
YMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ----
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
---------------------------------------------------
|
||||
>Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554
|
||||
PFFG--HNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLRE
|
||||
YMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWR
|
||||
ELHIHTAIIEQQISEVIQRNVN----YDLLSLFL-ASENELRDVAMNFIIAGRDTTAQLL
|
||||
SWFSYLLT-NP----KVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRY
|
||||
AKTDI-PLL---NIIRKGDCIIIPTYAMGRMPWLW-NNALTFDPSRFEYSPAQYPAFNIP
|
||||
PRLCLGKHVALLEAKIVIIKLLRKYR-IVAIPSVMKNGFKVRLELR-----
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
-------------------------------------------ITMNFIIAGKDTTAQLL
|
||||
SWFFYVITHNR--SDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRF
|
||||
AKSDIFRVD---YTIRKGDGIVIPLYAMGRMPWIW-ENPDEFDPLRFQFLPSEYPAFNIP
|
||||
PRLCLGKHVALMEAKIAVIKLLKKYR-FVTQESPMKNGYKVKLIPK-----
|
||||
>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554
|
||||
--------------------------LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRD
|
||||
YMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFK
|
||||
ELLFHEKTINNMVWDLVHKCKERL--CDLLSLFI-ITDVELRDITINFVIAGRDTTAQLL
|
||||
SWFSYLIT-WP----QVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVRE
|
||||
AKVDI-HLP---HIIRKGDGVIVPTYAMGRLPWLW-EKPEEMNPDRFQFTPSEYPAFNIP
|
||||
PRLCLGKHVSLMEAKIQIVKLLPKYK-FEPLPSAMKNGFKVKLVPRDTQ--
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------LRDVAMNFIIAGRDTTAQLL
|
||||
SWFMYLFT-NK----EIEKPILNEINSII-NYIDVKLKYLENCFFETLRLRPAVPHLLRF
|
||||
AKTDI-QLK---YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIP
|
||||
PRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------YVIRKGDGICIPTFAMNRMPWIW-DNPFKFDPNRFDQSPSKYVAFNIP
|
||||
PRLCLGKHVALLEAKLLVLELLTRFK-IEPVLSAMRNGFKVYFHPR-----
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------IKLNYLENSFLETLRLRPSVPHLVRK
|
||||
AVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIK
|
||||
PRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQT---
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
---------NQ----HVEDKIMDEINQHI-NYNTIKLNYLENSFLETLRLRPSVPHLVRK
|
||||
AVVDI-KIP---HIIRKDDTILVPTYAMGRMEWIW-KDALKFDPTRFEYSPSKYPAFNIK
|
||||
PRLCLGKHVALLEAKIAIVKLFKKYK-FIPIESLMKNGFRVKLIKRQTQF-
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------RVRAAQLL
|
||||
SWFLYEITENN----EILSNINNEINEYI-NYDNIKLVYLENCFLETLRLRPSVPHLVRQ
|
||||
ANVDI-NIP---YTIRKDDTIIVPTYAMGRMDYIW-ENPLKFDPNRFKHSPSKYPAFNIK
|
||||
PRLCLGKHVALLEAKIAIAKLFQKYK-FEPIKSVMKNGFKVKVVPNIFK--
|
||||
>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
-----------------------SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQ
|
||||
ANVDI-PIP---YTIRKDDTIIVPTYAMGRMDYIW-ENALTFDPNRFKYSPSKYPAFNIK
|
||||
PRLCLGKHVALLEAKIAIAKLFKKYK-FEPIKSVMKNGFKVKVVPIE----
|
||||
>Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554
|
||||
PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKD
|
||||
YMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYG
|
||||
ELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLL
|
||||
SWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRV
|
||||
AKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIP
|
||||
PRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
|
||||
>Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554
|
||||
PFIG--HNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKD
|
||||
YMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYG
|
||||
ELKKHEEIINKKIQDIISKRKEQ---YDIISIFL-ISDKELRDICANFILAGRDTTGQLL
|
||||
SWFCYEICENK----HIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRV
|
||||
AKTDI-LIP---HVIRKGDTIIVPCYAMGRMPTIW-KEPLKFDPLRFNFPPCKYPAFNIP
|
||||
PRLCLGKHVAIMEAKIAIVKLFRKYE-LIPDTSMMKTGFRVRLKSR-----
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------KQVQ--YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTL
|
||||
SWFTYELC--P----HVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRF
|
||||
ATRDF-RLP---HIIRKGDGIVCAAYLMGHISHLW-DDPERFDPTRFEYDPSYFPAFNIA
|
||||
PRICLGKHVALLEAKIAAIKLFKKFK-IIPVPAPMKNGFKVTLHNIETD--
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSLFL-MSIKELRDISMNFIIAGRDTTAQTL
|
||||
SWFIYELS--P----HVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRF
|
||||
ATRDF-RIP---HIIRKGDGIVCAAYIMGHVPELW-NNPHQFDPTRFEYDPSYFPAFNIA
|
||||
PRLCLGKHVALLEAKIAAVKLLKKFK-IIPVPAPMKNGFKVTLECRN----
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------IR--YDLLSLFL-ITEKELRDIAMNFIIAGRDTTAQTL
|
||||
SWFIYELT-SP----DVEENILKEIDS-IGTYENIKFKYLENALLETLRMHPAVPHLVRY
|
||||
ATRDI-LLR---NIVRKGDGIVVGAYVMGHIPWLW-PDPERFDPTRFEYDPCYFPVFNVA
|
||||
PRLCLGKHVALLEAKIAAVKLLKKYR-IEAIKAPMRYGFKVKLHPRL----
|
||||
>Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554
|
||||
PFIGHIKNFIFIVDPKIIDLLFD--KRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRD
|
||||
YMFKSFCSTTDEFINKLS-----VDIYDMYNRLTLEAFTYVAFGTNLGAIS---------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------QAPEELEF
|
||||
TSFDK-ICK------------------------------------RF-FDP---------
|
||||
------------------IKM------------------------------
|
||||
>Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQML
|
||||
SWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRT
|
||||
AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
|
||||
PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG-------------
|
||||
>Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSMFI-ITDQELRDITFSFIIAGKDTTAQML
|
||||
SWFMYHIHN----LQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRT
|
||||
AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
|
||||
PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
|
||||
>Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
---------------------------------KVKCSFIECCLKESLRLYPSVPHLVRT
|
||||
AVKDM-KLP---YTLRKGDELFVSTFAMGRMPWIW-KDPLEFKPERFAPDPSVYPAFNIA
|
||||
PRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK------
|
||||
>Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------EYEKVKCRYIECCLKESLRLYPSVPHLVRT
|
||||
AVKDI-KLP---YTVRPGDEVFVSAYAMGRMPWVW-EDPLEFKPERFQPDPSMYPAFNIA
|
||||
PRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK------
|
||||
>Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------FDLISMFI-ITDEELRDITFSFIIAGKDTTAQML
|
||||
SWLMYHLHK----LQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRT
|
||||
PVKDI-ATH---YVIRKGDEVMVAAYSMARMPWLW-DDPLAFKPERFMYDPSLYPAFNIA
|
||||
PRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR-----
|
||||
>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
---------------------------------------------INFIIAGKDTTAQML
|
||||
SWFFYHINN----LYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRT
|
||||
AVKDI-RTP---YVIRKGDEIFISAWSMGRAPWIW-DEPLQFKPERFMIDPSRFPAFNVA
|
||||
PRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE-----
|
||||
>Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554
|
||||
PFVG--HHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRD
|
||||
YMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKK
|
||||
EMRSHIDWIEDYIYKVIANRRAYY--YDLLSMFL-ISDKELRDITVNFIIAGKDTTAQML
|
||||
SWFTYHLHK----LIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARA
|
||||
AVVDI-ETY---YTIRAGDEVLICPLSMSRLEWIW-PNAEQFIPERFAFDPWVYPAFNIP
|
||||
PRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP--
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRT
|
||||
AIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLK
|
||||
PRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
-------------------------------------------------IAGRDTTSQML
|
||||
SWFMFHLTKND-GMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRT
|
||||
AIEDI-KLP---HTIRKGEEIVISTYSMGRSKYIW-EDPMKFNPERFIYEPWVYPAFNLK
|
||||
PRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK-------
|
||||
>Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSMFI-ISDRQLRDITMNFIIAGRDTTSQML
|
||||
SWFMYHLTNSD--MKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRT
|
||||
AIEDI-QTP---YTIRKNDEIMISTYSIGRSKYIW-KDPLTFNPERFLYDPSVYPAFNLK
|
||||
PRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE-------
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSMFI-ISDDELRDITMNFIIAGRDTTSHML
|
||||
SWFLFHLTQND-GMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRT
|
||||
AVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DKPLKFDANRFIYDASVYPAFNIQ
|
||||
PRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK-------
|
||||
>Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------------ML
|
||||
SWFYFHLTQND-GMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRT
|
||||
AVEDI-KTK---YTIRKGDDIVISAYAMGRSKYIW-DDPLKFDANRFIYDASVYPAFNIQ
|
||||
PRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK-------
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------VECKYIECCLKETLRLYPSVPHFSRE
|
||||
MVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-ENADKFIPERFMYDNSQYPAFNIA
|
||||
PRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM----------------
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSRE
|
||||
MVKDF-KVKI--YTFYKGDEIIITTFPLGRLPWLW-GNADKFIPERFMYDNSQYPAFNIA
|
||||
PRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH-------
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSRE
|
||||
MVKDF-KLKI--YTFYKGDEIVVTTFAMGRLPWLW-KNAEKFVPERFMYDQSKYVAFNIS
|
||||
PRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE-------
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
-------------------------------------------------IAGRDTTSQMI
|
||||
SWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQ
|
||||
MVTDL-TLNI--YTFEKGDEIVVFTIALGKLPWLW-ENADEFIPERFIYDAEIWPAFNIA
|
||||
PRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD-------
|
||||
>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YDLLSIFI-INDKFLRDVTMNFIIAGRDTTSQML
|
||||
SWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVRE
|
||||
MVSDL-TLNI--YTFHKGDEVIVCTIALGKLPWLW-ENANEFIPERFIYDAHIWPAFNIA
|
||||
PRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK-------
|
||||
>Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
------------------------------------------DITMNFIIAGRDTTSQML
|
||||
SWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVRE
|
||||
MVTDM-KINI--YIFEKGNEIIICTIALGKLPWLW-DNANEFIPERFIYDNHIYPAFNIL
|
||||
PRTCLGKNVALLEGKIAIISMFSNFNKFKAVP-------------------
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------------LL
|
||||
SWFLYLVYENG--KKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERT
|
||||
AVEDI-KLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIA
|
||||
PRICLGKHVALLEAKLVVIKLLRHFT-IQPVKSAMKNGYKIILKRR-----
|
||||
>Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554
|
||||
------QNVVFISDPVQTKYIYD--RRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKH
|
||||
YMFENFETCSKRLVNKLP-----IDLFDMFNRLTMDGFVASAFGVYSDTIE---------
|
||||
------------------------------------------------------------
|
||||
----------------------------------------------------QAPHDTRF
|
||||
EAFDG-GCD------------------------------------RFIARP---------
|
||||
-----------------FLETLKHAKRFCSIRERIESGE------------
|
||||
>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
-------------------ERIES--HDLLSLFM-FTEEELQDLCLNFIIAGRDTTAENI
|
||||
SWLMYELSKNP----HVLQLVIDEINTL--TYDNVELTYLESALLETQRLHPSVPTLNRQ
|
||||
AKRDI-KLP---FTVKKGDIYMVHNYAMGRAPWIW-EDPLRFDPTRFSYEPQVFPQFNIA
|
||||
PRMCLGKHVAMME--------------------------------------
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
--------------------------YNLLSLFLNYTLDELRDICINFIIAGRDTTAETL
|
||||
TWLCVELSSHP----DIVDQIRNEINQV--TYESLEMKYTESALLETQRLHPSVPSLIRF
|
||||
AFQDI-VLP---YTIRKGDAVNVFNYAMGRSPWIW-ENPLQFHPPRFQFHPSVYPAFNIG
|
||||
QRLCLGRHVALMHAKVVLYHLFKHFN-FKAVPAPLKNGFQVHLQPLHPTQN
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554
|
||||
------------------------------------------------------------
|
||||
------------------------------------------------------------
|
||||
---------------------------DLLTLYA-ITRSELQDVCVNFIIAGRDTTALNL
|
||||
CWLFILLAQNP----HCLQQLKDEIRSI--SFKTLDMTYTESCILEAQRIYPSVPSLTRV
|
||||
AVTDI-PLP---YVIHKDEIVVISTFAMNRSPKIW-ENPLQFDPSRFEHEPHIYPSFNIG
|
||||
QRLCLGRHVALLVAKVVLYHFFQNFD-FQIDMAPLTNGLPMRIIPLSSSV-
|
||||
@ -1 +0,0 @@
|
||||
((seq0017:0.159520,((((seq0029:0.000335,seq0030:0.000001):0.298687,((seq0026:0.118374,((seq0022:0.000001,(seq0021:0.000001,(seq0020:0.000001,(seq0023:0.000001,seq0024:0.000001):0.003307):0.001691):0.000865):0.194370,(seq0019:0.213074,(seq0047:0.000001,(seq0040:0.218288,seq0060:0.741067):0.558436):0.264600):0.089062):0.026603):0.078072,(((seq0059:0.416185,(((seq0051:0.002343,seq0052:0.051365):0.156768,(seq0050:0.102723,(seq0048:0.000001,seq0049:0.000606):0.156109):0.026679):0.088477,(seq0046:0.251155,(((seq0055:0.122540,(seq0053:0.000001,seq0054:0.050064):0.060836):0.112993,(seq0058:0.094203,(seq0056:0.146811,seq0057:0.074128):0.032205):0.099845):0.238408,(seq0045:0.176854,(seq0044:0.062128,(seq0041:0.000001,(seq0042:0.014202,seq0043:0.000001):0.007922):0.069848):0.072547):0.053735):0.020337):0.040887):0.078664):0.063075,((seq0039:0.164075,(seq0037:0.088700,seq0038:0.060206):0.105530):0.093641,((seq0000:0.095561,seq0001:0.071802):0.371565,(seq0061:0.262548,(seq0062:0.274390,(seq0025:0.000001,seq0063:0.456008):0.072702):0.040402):0.114369):0.042115):0.053357):0.040190,(seq0027:0.279481,seq0028:0.236863):0.026728):0.009003):0.005029):0.027732,(seq0018:0.176464,((seq0035:0.000001,seq0036:0.000001):0.279842,((seq0033:0.064803,seq0034:0.034665):0.126784,(seq0031:0.000001,seq0032:0.021257):0.110018):0.058727):0.055398):0.008537):0.026864,(seq0015:0.079754,seq0016:0.205938):0.020846):0.015120):0.020439,((seq0009:0.022972,seq0010:0.000001):0.164226,(seq0014:0.189401,(seq0011:0.000001,(seq0012:0.012592,seq0013:0.000001):0.003812):0.062063):0.019146):0.014995,(seq0008:0.161694,((seq0007:0.000001,(seq0005:0.000001,seq0006:0.000001):0.002884):0.117868,(seq0002:0.000001,(seq0003:0.002943,seq0004:0.003582):0.007856):0.097737):0.007560):0.006500);
|
||||
@ -1,10 +0,0 @@
|
||||
2.000817428956
|
||||
2.58462865668747
|
||||
1.49936059497511
|
||||
1.23331485380722
|
||||
2.15783221114012
|
||||
2.90590667209469
|
||||
2.63676633992571
|
||||
2.80645936921989
|
||||
1.84405518368005
|
||||
2.13819830457351
|
||||
@ -1,64 +0,0 @@
|
||||
Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554 seq0000
|
||||
Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554 seq0001
|
||||
Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554 seq0002
|
||||
Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554 seq0003
|
||||
Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554 seq0004
|
||||
Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554 seq0005
|
||||
Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554 seq0006
|
||||
Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554 seq0007
|
||||
Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554 seq0008
|
||||
Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554 seq0009
|
||||
Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554 seq0010
|
||||
Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554 seq0011
|
||||
Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554 seq0012
|
||||
Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554 seq0013
|
||||
Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554 seq0014
|
||||
Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554 seq0015
|
||||
Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554 seq0016
|
||||
Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554 seq0017
|
||||
Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554 seq0018
|
||||
Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554 seq0019
|
||||
Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554 seq0020
|
||||
Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554 seq0021
|
||||
Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554 seq0022
|
||||
Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554 seq0023
|
||||
Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554 seq0024
|
||||
Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554 seq0025
|
||||
Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554 seq0026
|
||||
Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554 seq0027
|
||||
Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554 seq0028
|
||||
Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554 seq0029
|
||||
Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554 seq0030
|
||||
Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554 seq0031
|
||||
Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554 seq0032
|
||||
Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554 seq0033
|
||||
Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554 seq0034
|
||||
Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554 seq0035
|
||||
Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554 seq0036
|
||||
Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554 seq0037
|
||||
Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554 seq0038
|
||||
Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554 seq0039
|
||||
Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554 seq0040
|
||||
Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554 seq0041
|
||||
Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554 seq0042
|
||||
Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554 seq0043
|
||||
Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554 seq0044
|
||||
Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554 seq0045
|
||||
Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554 seq0046
|
||||
Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554 seq0047
|
||||
Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554 seq0048
|
||||
Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554 seq0049
|
||||
Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554 seq0050
|
||||
Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554 seq0051
|
||||
Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554 seq0052
|
||||
Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554 seq0053
|
||||
Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554 seq0054
|
||||
Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554 seq0055
|
||||
Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554 seq0056
|
||||
Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554 seq0057
|
||||
Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554 seq0058
|
||||
Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554 seq0059
|
||||
Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554 seq0060
|
||||
Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554 seq0061
|
||||
Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554 seq0062
|
||||
Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554 seq0063
|
||||
@ -1,192 +0,0 @@
|
||||
>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554
|
||||
ISFDASVFKWGELAAHMKVVDGFADEMIAKCRYDLLSKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCRNPEIQSKIYDELKTYQTVKMKYLEAVLYESLRLHPSVPNMTRFATRDIQLNNTIRKGDAVLVSNYVLGRLQKWWDNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKHVAMMEAKIGLATILKDYRMELKPGPMKNGCYINFIDRLSE
|
||||
|
||||
>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554
|
||||
YDLLTKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNPEIQDKVYEELSTYQSVKMKYLEAVLYEALRLHPSVPNMSRFATRDIQLSDVIRKGDCILVSNYVLGRLHQWWENALQFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYRMELKPGPMKNGCFINFIDRSTK
|
||||
|
||||
>Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554
|
||||
IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
|
||||
|
||||
>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554
|
||||
LLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVNLIPR
|
||||
|
||||
>Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554
|
||||
ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
|
||||
|
||||
>Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
|
||||
|
||||
>Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
|
||||
|
||||
>Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPR
|
||||
|
||||
>Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554
|
||||
PYFGHHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTLKAHVKVINEFAERIIRSKRKDYYDIMSLFLISDQELRDMALNFIIAGRDTTAQLLSWFSYAMTENADVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDIDLPETIRKGNGIVIPTFAMGRMPWIWKDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEAKIAVVKLFTKYKLVPMPSVMKNGFKVKLIPRE
|
||||
|
||||
>Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554
|
||||
LMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
|
||||
|
||||
>Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554
|
||||
YDLMSLFLISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
|
||||
|
||||
>Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554
|
||||
YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKNGFKVRLVPRCK
|
||||
|
||||
>Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554
|
||||
RSSSKKQHFYDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLDALPSVMKNGFKVRLVPRCK
|
||||
|
||||
>Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554
|
||||
YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKNGFKVRLVPRCK
|
||||
|
||||
>Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554
|
||||
MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDIPLPDVIRKGDGVIVPMYAMGRMPWLWKNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFKLEALPTVMKNGFKVKLIPRCK
|
||||
|
||||
>Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554
|
||||
YDLMSLFLITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNKQIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDIKLPDIIRKGDGIVIPTYAMGRMPWIWNDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLQPLPSIMRNGFKVKLIPRDSK
|
||||
|
||||
>Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554
|
||||
PLIGHNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSLKKHSHILNDFAKKVIDDRKSYDLLSLFLVNVSELRDVCINFIVAGRDTTAQLLSWFMYELSNPKIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDIELPGHIIRKGDGIVIPTYAMGRMPWIWKDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKIAIVKLFKKYKLVKLPSVMKYGYKVKLEPRNQ
|
||||
|
||||
>Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554
|
||||
FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKHLKIINEFASNIIHKKRQQFYDLISLFMITDEELRDIALNFIIAGRDTTAQLLSWFSYLVTENESVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDIKLPHIIRKGDGIVIPTFAMGRMPWIWSNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIAIIKLFKKYKLEAVPSVMKYGFNVKLVPRKQET
|
||||
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554
|
||||
NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERKFDLLSLFLTSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRFAKVDILLPHVIRKGDGIVVPTYAMGRMPSLWKDPLKFDPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFKLEPLSSIMKNGFRVKLVPR
|
||||
|
||||
>Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554
|
||||
KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQYKDLLTLYFATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHAHVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRFALVDIKLPHVIRKGDGVVVPVYAMGRMPWLWPKPLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYRIVARESIMKDGFYARLQPRAQQQQ
|
||||
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554
|
||||
MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554
|
||||
MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554
|
||||
PFFGHNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ
|
||||
|
||||
>Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554
|
||||
PFFGHNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWRELHIHTAIIEQQISEVIQRNVNYDLLSLFLASENELRDVAMNFIIAGRDTTAQLLSWFSYLLTNPKVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDIPLLNIIRKGDCIIIPTYAMGRMPWLWNNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIVIIKLLRKYRIVAIPSVMKNGFKVRLELR
|
||||
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554
|
||||
ITMNFIIAGKDTTAQLLSWFFYVITHNRSDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRFAKSDIFRVDYTIRKGDGIVIPLYAMGRMPWIWENPDEFDPLRFQFLPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYRFVTQESPMKNGYKVKLIPK
|
||||
|
||||
>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554
|
||||
LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERLCDLLSLFIITDVELRDITINFVIAGRDTTAQLLSWFSYLITWPQVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVREAKVDIHLPHIIRKGDGVIVPTYAMGRLPWLWEKPEEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYKFEPLPSAMKNGFKVKLVPRDTQ
|
||||
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554
|
||||
LRDVAMNFIIAGRDTTAQLLSWFMYLFTNKEIEKPILNEINSIINYIDVKLKYLENCFFETLRLRPAVPHLLRFAKTDIQLKYVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
|
||||
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554
|
||||
YVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
|
||||
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554
|
||||
IKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFRVKLIKRQT
|
||||
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554
|
||||
NQHVEDKIMDEINQHINYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFRVKLIKRQTQF
|
||||
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554
|
||||
RVRAAQLLSWFLYEITENNEILSNINNEINEYINYDNIKLVYLENCFLETLRLRPSVPHLVRQANVDINIPYTIRKDDTIIVPTYAMGRMDYIWENPLKFDPNRFKHSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFQKYKFEPIKSVMKNGFKVKVVPNIFK
|
||||
|
||||
>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554
|
||||
SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDIPIPYTIRKDDTIIVPTYAMGRMDYIWENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYKFEPIKSVMKNGFKVKVVPIE
|
||||
|
||||
>Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554
|
||||
PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYEICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHVIRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYELIPDTSMMKTGFRVRLKSR
|
||||
|
||||
>Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554
|
||||
PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYEICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHVIRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYELIPDTSMMKTGFRVRLKSR
|
||||
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554
|
||||
KQVQYDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFTYELCPHVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDFRLPHIIRKGDGIVCAAYLMGHISHLWDDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFKIIPVPAPMKNGFKVTLHNIETD
|
||||
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554
|
||||
YDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFIYELSPHVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRFATRDFRIPHIIRKGDGIVCAAYIMGHVPELWNNPHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFKIIPVPAPMKNGFKVTLECRN
|
||||
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554
|
||||
IRYDLLSLFLITEKELRDIAMNFIIAGRDTTAQTLSWFIYELTSPDVEENILKEIDSIGTYENIKFKYLENALLETLRMHPAVPHLVRYATRDILLRNIVRKGDGIVVGAYVMGHIPWLWPDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYRIEAIKAPMRYGFKVKLHPRL
|
||||
|
||||
>Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554
|
||||
PFIGHIKNFIFIVDPKIIDLLFDKRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYMFKSFCSTTDEFINKLSVDIYDMYNRLTLEAFTYVAFGTNLGAISQAPEELEFTSFDKICKRFFDPIKM
|
||||
|
||||
>Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554
|
||||
YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG
|
||||
|
||||
>Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554
|
||||
YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK
|
||||
|
||||
>Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554
|
||||
KVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK
|
||||
|
||||
>Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554
|
||||
EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDIKLPYTVRPGDEVFVSAYAMGRMPWVWEDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK
|
||||
|
||||
>Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554
|
||||
FDLISMFIITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHKLQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDIATHYVIRKGDEVMVAAYSMARMPWLWDDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR
|
||||
|
||||
>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554
|
||||
INFIIAGKDTTAQMLSWFFYHINNLYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRTAVKDIRTPYVIRKGDEIFISAWSMGRAPWIWDEPLQFKPERFMIDPSRFPAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE
|
||||
|
||||
>Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554
|
||||
PFVGHHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEMRSHIDWIEDYIYKVIANRRAYYYDLLSMFLISDKELRDITVNFIIAGKDTTAQMLSWFTYHLHKLIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDIETYYTIRAGDEVLICPLSMSRLEWIWPNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP
|
||||
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554
|
||||
IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
|
||||
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554
|
||||
IAGRDTTSQMLSWFMFHLTKNDGMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
|
||||
|
||||
>Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554
|
||||
YDLLSMFIISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSDMKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDIQTPYTIRKNDEIMISTYSIGRSKYIWKDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE
|
||||
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554
|
||||
YDLLSMFIISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQNDGMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK
|
||||
|
||||
>Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554
|
||||
MLSWFYFHLTQNDGMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDDPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK
|
||||
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554
|
||||
VECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWENADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM
|
||||
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554
|
||||
IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWGNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH
|
||||
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554
|
||||
IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDFKLKIYTFYKGDEIVVTTFAMGRLPWLWKNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE
|
||||
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554
|
||||
IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQMVTDLTLNIYTFEKGDEIVVFTIALGKLPWLWENADEFIPERFIYDAEIWPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD
|
||||
|
||||
>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554
|
||||
YDLLSIFIINDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDLTLNIYTFHKGDEVIVCTIALGKLPWLWENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK
|
||||
|
||||
>Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554
|
||||
DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVREMVTDMKINIYIFEKGNEIIICTIALGKLPWLWDNANEFIPERFIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP
|
||||
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554
|
||||
LLSWFLYLVYENGKKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERTAVEDIKLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAPRICLGKHVALLEAKLVVIKLLRHFTIQPVKSAMKNGYKIILKRR
|
||||
|
||||
>Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554
|
||||
QNVVFISDPVQTKYIYDRRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFETCSKRLVNKLPIDLFDMFNRLTMDGFVASAFGVYSDTIEQAPHDTRFEAFDGGCDRFIARPFLETLKHAKRFCSIRERIESGE
|
||||
|
||||
>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554
|
||||
ERIESHDLLSLFMFTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNPHVLQLVIDEINTLTYDNVELTYLESALLETQRLHPSVPTLNRQAKRDIKLPFTVKKGDIYMVHNYAMGRAPWIWEDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME
|
||||
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554
|
||||
YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHPDIVDQIRNEINQVTYESLEMKYTESALLETQRLHPSVPSLIRFAFQDIVLPYTIRKGDAVNVFNYAMGRSPWIWENPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFNFKAVPAPLKNGFQVHLQPLHPTQN
|
||||
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554
|
||||
DLLTLYAITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNPHCLQQLKDEIRSISFKTLDMTYTESCILEAQRIYPSVPSLTRVAVTDIPLPYVIHKDEIVVISTFAMNRSPKIWENPLQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFDFQIDMAPLTNGLPMRIIPLSSSV
|
||||
|
||||
@ -1,128 +0,0 @@
|
||||
>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554
|
||||
ISFDASVFKWGELAAHMKVVDGFADEMIAKCRYDLLSKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCRNPEIQSKIYDELKTYQTVKMKYLEAVLYESLRLHPSVPNMTRFATRDIQLNNTIRKGDAVLVSNYVLGRLQKWWDNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKHVAMMEAKIGLATILKDYRMELKPGPMKNGCYINFIDRLSE
|
||||
>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554
|
||||
YDLLTKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNPEIQDKVYEELSTYQSVKMKYLEAVLYEALRLHPSVPNMSRFATRDIQLSDVIRKGDCILVSNYVLGRLHQWWENALQFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYRMELKPGPMKNGCFINFIDRSTK
|
||||
>Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554
|
||||
IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKCELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
|
||||
>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554
|
||||
LLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVNLIPR
|
||||
>Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554
|
||||
ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
|
||||
>Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
|
||||
>Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
|
||||
>Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYMFEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTLKKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTYLLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPDIIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEPVSSVMKNGFKVKLIPR
|
||||
>Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554
|
||||
PYFGHHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYMFQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTLKAHVKVINEFAERIIRSKRKDYYDIMSLFLISDQELRDMALNFIIAGRDTTAQLLSWFSYAMTENADVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDIDLPETIRKGNGIVIPTFAMGRMPWIWKDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEAKIAVVKLFTKYKLVPMPSVMKNGFKVKLIPRE
|
||||
>Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554
|
||||
LMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
|
||||
>Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554
|
||||
YDLMSLFLISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
|
||||
>Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554
|
||||
YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKNGFKVRLVPRCK
|
||||
>Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554
|
||||
RSSSKKQHFYDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLDALPSVMKNGFKVRLVPRCK
|
||||
>Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554
|
||||
YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKNGFKVRLVPRCK
|
||||
>Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554
|
||||
MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDIPLPDVIRKGDGVIVPMYAMGRMPWLWKNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFKLEALPTVMKNGFKVKLIPRCK
|
||||
>Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554
|
||||
YDLMSLFLITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNKQIEENIMNEINQYIGDYNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDIKLPDIIRKGDGIVIPTYAMGRMPWIWNDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLQPLPSIMRNGFKVKLIPRDSK
|
||||
>Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554
|
||||
PLIGHNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYMFNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSLKKHSHILNDFAKKVIDDRKSYDLLSLFLVNVSELRDVCINFIVAGRDTTAQLLSWFMYELSNPKIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDIELPGHIIRKGDGIVIPTYAMGRMPWIWKDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKIAIVKLFKKYKLVKLPSVMKYGYKVKLEPRNQ
|
||||
>Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554
|
||||
FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKHLKIINEFASNIIHKKRQQFYDLISLFMITDEELRDIALNFIIAGRDTTAQLLSWFSYLVTENESVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDIKLPHIIRKGDGIVIPTFAMGRMPWIWSNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIAIIKLFKKYKLEAVPSVMKYGFNVKLVPRKQET
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554
|
||||
NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERKFDLLSLFLTSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQECEAKVTKEIMEHVPTYEMVKCQYLENALLETLRLRPSVPHLVRFAKVDILLPHVIRKGDGIVVPTYAMGRMPSLWKDPLKFDPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFKLEPLSSIMKNGFRVKLVPR
|
||||
>Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554
|
||||
KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDLYNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQYKDLLTLYFATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHAHVDARILEEIHTYVGTYQMVKLKYMESCFLETLRLHPSVPHLVRFALVDIKLPHVIRKGDGVVVPVYAMGRMPWLWPKPLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYRIVARESIMKDGFYARLQPRAQQQQ
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554
|
||||
MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554
|
||||
MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
>Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554
|
||||
PFFGHNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYMFEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ
|
||||
>Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554
|
||||
PFFGHNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYMFEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWRELHIHTAIIEQQISEVIQRNVNYDLLSLFLASENELRDVAMNFIIAGRDTTAQLLSWFSYLLTNPKVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDIPLLNIIRKGDCIIIPTYAMGRMPWLWNNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIVIIKLLRKYRIVAIPSVMKNGFKVRLELR
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554
|
||||
ITMNFIIAGKDTTAQLLSWFFYVITHNRSDEVISNILNEFDAQSNGYEKMKLQYLEYCLLETLRLFPSVPHLIRFAKSDIFRVDYTIRKGDGIVIPLYAMGRMPWIWENPDEFDPLRFQFLPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYRFVTQESPMKNGYKVKLIPK
|
||||
>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554
|
||||
LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDLYDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERLCDLLSLFIITDVELRDITINFVIAGRDTTAQLLSWFSYLITWPQVEKKVLKEIKEVFPDYGKIKLEYLENAFLETLRMHPSVPHLVREAKVDIHLPHIIRKGDGVIVPTYAMGRLPWLWEKPEEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYKFEPLPSAMKNGFKVKLVPRDTQ
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554
|
||||
LRDVAMNFIIAGRDTTAQLLSWFMYLFTNKEIEKPILNEINSIINYIDVKLKYLENCFFETLRLRPAVPHLLRFAKTDIQLKYVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554
|
||||
YVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554
|
||||
IKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFRVKLIKRQT
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554
|
||||
NQHVEDKIMDEINQHINYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFRVKLIKRQTQF
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554
|
||||
RVRAAQLLSWFLYEITENNEILSNINNEINEYINYDNIKLVYLENCFLETLRLRPSVPHLVRQANVDINIPYTIRKDDTIIVPTYAMGRMDYIWENPLKFDPNRFKHSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFQKYKFEPIKSVMKNGFKVKVVPNIFK
|
||||
>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554
|
||||
SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDIPIPYTIRKDDTIIVPTYAMGRMDYIWENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYKFEPIKSVMKNGFKVKVVPIE
|
||||
>Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554
|
||||
PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYEICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHVIRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYELIPDTSMMKTGFRVRLKSR
|
||||
>Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554
|
||||
PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYMFEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGELKKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYEICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHVIRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAKIAIVKLFRKYELIPDTSMMKTGFRVRLKSR
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554
|
||||
KQVQYDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFTYELCPHVYDQIMKEIDQVIGTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDFRLPHIIRKGDGIVCAAYLMGHISHLWDDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFKIIPVPAPMKNGFKVTLHNIETD
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554
|
||||
YDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFIYELSPHVQDQIMNEINHVIGDYHLIKLKYLENALLETLRLHPAVPHLLRFATRDFRIPHIIRKGDGIVCAAYIMGHVPELWNNPHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFKIIPVPAPMKNGFKVTLECRN
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554
|
||||
IRYDLLSLFLITEKELRDIAMNFIIAGRDTTAQTLSWFIYELTSPDVEENILKEIDSIGTYENIKFKYLENALLETLRMHPAVPHLVRYATRDILLRNIVRKGDGIVVGAYVMGHIPWLWPDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYRIEAIKAPMRYGFKVKLHPRL
|
||||
>Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554
|
||||
PFIGHIKNFIFIVDPKIIDLLFDKRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYMFKSFCSTTDEFINKLSVDIYDMYNRLTLEAFTYVAFGTNLGAISQAPEELEFTSFDKICKRFFDPIKM
|
||||
>Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554
|
||||
YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG
|
||||
>Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554
|
||||
YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGEYDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK
|
||||
>Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554
|
||||
KVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAGFQAHLQK
|
||||
>Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554
|
||||
EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDIKLPYTVRPGDEVFVSAYAMGRMPWVWEDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPMGAGFQAHLQK
|
||||
>Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554
|
||||
FDLISMFIITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHKLQQVMDNIRAEIRRVFGDYEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDIATHYVIRKGDEVMVAAYSMARMPWLWDDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPMETGFKAHLNVR
|
||||
>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554
|
||||
INFIIAGKDTTAQMLSWFFYHINNLYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLRLYPSVPHLVRTAVKDIRTPYVIRKGDEIFISAWSMGRAPWIWDEPLQFKPERFMIDPSRFPAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE
|
||||
>Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554
|
||||
PFVGHHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYMFDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEMRSHIDWIEDYIYKVIANRRAYYYDLLSMFLISDKELRDITVNFIIAGKDTTAQMLSWFTYHLHKLIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDIETYYTIRAGDEVLICPLSMSRLEWIWPNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEGKIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554
|
||||
IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554
|
||||
IAGRDTTSQMLSWFMFHLTKNDGMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
|
||||
>Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554
|
||||
YDLLSMFIISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSDMKTIESNIRNEIKTIFGTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDIQTPYTIRKNDEIMISTYSIGRSKYIWKDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSAMKNGWKVTLE
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554
|
||||
YDLLSMFIISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQNDGMSDIEKKIRNEIDNIFGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPSAMKNGWKLDLK
|
||||
>Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554
|
||||
MLSWFYFHLTQNDGMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDDPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554
|
||||
VECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWENADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554
|
||||
IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWGNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAMDGGFKIHIH
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554
|
||||
IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDFKLKIYTFYKGDEIVVTTFAMGRLPWLWKNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIAMFSQFKSFRTVPAAMDGGFNIYVE
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554
|
||||
IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLRLYPSVPHFVRQMVTDLTLNIYTFEKGDEIVVFTIALGKLPWLWENADEFIPERFIYDAEIWPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD
|
||||
>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554
|
||||
YDLLSIFIINDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVDVFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDLTLNIYTFHKGDEVIVCTIALGKLPWLWENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTVPAPFRNGFNIYLK
|
||||
>Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554
|
||||
DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEACLKETLRMYPSVPHFVREMVTDMKINIYIFEKGNEIIICTIALGKLPWLWDNANEFIPERFIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554
|
||||
LLSWFLYLVYENGKKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERTAVEDIKLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAPRICLGKHVALLEAKLVVIKLLRHFTIQPVKSAMKNGYKIILKRR
|
||||
>Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554
|
||||
QNVVFISDPVQTKYIYDRRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFETCSKRLVNKLPIDLFDMFNRLTMDGFVASAFGVYSDTIEQAPHDTRFEAFDGGCDRFIARPFLETLKHAKRFCSIRERIESGE
|
||||
>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554
|
||||
ERIESHDLLSLFMFTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNPHVLQLVIDEINTLTYDNVELTYLESALLETQRLHPSVPTLNRQAKRDIKLPFTVKKGDIYMVHNYAMGRAPWIWEDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554
|
||||
YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHPDIVDQIRNEINQVTYESLEMKYTESALLETQRLHPSVPSLIRFAFQDIVLPYTIRKGDAVNVFNYAMGRSPWIWENPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFNFKAVPAPLKNGFQVHLQPLHPTQN
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554
|
||||
DLLTLYAITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNPHCLQQLKDEIRSISFKTLDMTYTESCILEAQRIYPSVPSLTRVAVTDIPLPYVIHKDEIVVISTFAMNRSPKIWENPLQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFDFQIDMAPLTNGLPMRIIPLSSSV
|
||||
@ -1,20 +0,0 @@
|
||||
>seq0025
|
||||
PFFGHNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYM
|
||||
FEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ
|
||||
|
||||
>seq0040
|
||||
PFIGHIKNFIFIVDPKIIDLLFDKRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYM
|
||||
FKSFCSTTDEFINKLSVDIYDMYNRLTLEAFTYVAFGTNLGAISQAPEELEFTSFDKICK
|
||||
RFFDPIKM
|
||||
|
||||
>seq0060
|
||||
QNVVFISDPVQTKYIYDRRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFET
|
||||
CSKRLVNKLPIDLFDMFNRLTMDGFVASAFGVYSDTIEQAPHDTRFEAFDGGCDRFIARP
|
||||
FLETLKHAKRFCSIRERIESGE
|
||||
|
||||
>seq0063
|
||||
DLLTLYAITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNPHCLQQLKDEIRSISFKT
|
||||
LDMTYTESCILEAQRIYPSVPSLTRVAVTDIPLPYVIHKDEIVVISTFAMNRSPKIWENP
|
||||
LQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFDFQIDMAPLTNGLP
|
||||
MRIIPLSSSV
|
||||
|
||||
@ -1,20 +0,0 @@
|
||||
>Sr_rh_Pina_XX_Contig_8772_Len858_Cov33_OG5_126554
|
||||
PFFGHNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYM
|
||||
FEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ
|
||||
|
||||
>Sr_rh_Ssp1_XX_Contig_1307_Len810_Cov61_OG5_126554
|
||||
PFIGHIKNFIFIVDPKIIDLLFDKRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYM
|
||||
FKSFCSTTDEFINKLSVDIYDMYNRLTLEAFTYVAFGTNLGAISQAPEELEFTSFDKICK
|
||||
RFFDPIKM
|
||||
|
||||
>Sr_rh_Hhir_XX_Contig_20411_Len594_Cov57_OG5_126554
|
||||
QNVVFISDPVQTKYIYDRRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFET
|
||||
CSKRLVNKLPIDLFDMFNRLTMDGFVASAFGVYSDTIEQAPHDTRFEAFDGGCDRFIARP
|
||||
FLETLKHAKRFCSIRERIESGE
|
||||
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18519_Len663_Cov18_OG5_126554
|
||||
DLLTLYAITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNPHCLQQLKDEIRSISFKT
|
||||
LDMTYTESCILEAQRIYPSVPSLTRVAVTDIPLPYVIHKDEIVVISTFAMNRSPKIWENP
|
||||
LQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFDFQIDMAPLTNGLP
|
||||
MRIIPLSSSV
|
||||
|
||||
@ -1,366 +0,0 @@
|
||||
>seq0000
|
||||
ISFDASVFKWGELAAHMKVVDGFADEMIAKCRYDLLSKFIISTRELRDILLNFIIAGRDT
|
||||
TAQLLSWCSYELCRNPEIQSKIYDELKTYQTVKMKYLEAVLYESLRLHPSVPNMTRFATR
|
||||
DIQLNNTIRKGDAVLVSNYVLGRLQKWWDNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKH
|
||||
VAMMEAKIGLATILKDYRMELKPGPMKNGCYINFIDRLSE
|
||||
|
||||
>seq0001
|
||||
YDLLTKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNPEIQDKVYEELSTYQSV
|
||||
KMKYLEAVLYEALRLHPSVPNMSRFATRDIQLSDVIRKGDCILVSNYVLGRLHQWWENAL
|
||||
QFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYRMELKPGPMKNGCFI
|
||||
NFIDRSTK
|
||||
|
||||
>seq0002
|
||||
IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKC
|
||||
ELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTII
|
||||
QKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMRE
|
||||
IEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAM
|
||||
GRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEA
|
||||
VPSVMKYGFKVKLIPR
|
||||
|
||||
>seq0003
|
||||
LLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAK
|
||||
VDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGK
|
||||
HVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVNLIPR
|
||||
|
||||
>seq0004
|
||||
ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAG
|
||||
RDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPH
|
||||
LIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPP
|
||||
RLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
|
||||
|
||||
>seq0005
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
|
||||
FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
|
||||
KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
|
||||
LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
|
||||
IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
|
||||
|
||||
>seq0006
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
|
||||
FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
|
||||
KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
|
||||
LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
|
||||
IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
|
||||
|
||||
>seq0007
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
|
||||
FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
|
||||
KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
|
||||
LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
|
||||
IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPR
|
||||
|
||||
>seq0008
|
||||
PYFGHHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYM
|
||||
FQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTL
|
||||
KAHVKVINEFAERIIRSKRKDYYDIMSLFLISDQELRDMALNFIIAGRDTTAQLLSWFSY
|
||||
AMTENADVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDIDLPE
|
||||
TIRKGNGIVIPTFAMGRMPWIWKDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAVVKLFTKYKLVPMPSVMKNGFKVKLIPRE
|
||||
|
||||
>seq0009
|
||||
LMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAK
|
||||
VDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGK
|
||||
HVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
|
||||
|
||||
>seq0010
|
||||
YDLMSLFLISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENEEVEKKIVEEIRLYVGD
|
||||
YNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIW
|
||||
KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKN
|
||||
GLKVRLIPRGK
|
||||
|
||||
>seq0011
|
||||
YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
|
||||
YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
|
||||
KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
|
||||
GFKVRLVPRCK
|
||||
|
||||
>seq0012
|
||||
RSSSKKQHFYDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIM
|
||||
QEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTY
|
||||
AMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKL
|
||||
DALPSVMKNGFKVRLVPRCK
|
||||
|
||||
>seq0013
|
||||
YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
|
||||
YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
|
||||
KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
|
||||
GFKVRLVPRCK
|
||||
|
||||
>seq0014
|
||||
MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDIPLPDVIRKGDGVIVPMYAM
|
||||
GRMPWLWKNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFKLEA
|
||||
LPTVMKNGFKVKLIPRCK
|
||||
|
||||
>seq0015
|
||||
YDLMSLFLITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNKQIEENIMNEINQYIGD
|
||||
YNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDIKLPDIIRKGDGIVIPTYAMGRMPWIW
|
||||
NDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLQPLPSIMRN
|
||||
GFKVKLIPRDSK
|
||||
|
||||
>seq0016
|
||||
PLIGHNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYM
|
||||
FNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSL
|
||||
KKHSHILNDFAKKVIDDRKSYDLLSLFLVNVSELRDVCINFIVAGRDTTAQLLSWFMYEL
|
||||
SNPKIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDIELPGHII
|
||||
RKGDGIVIPTYAMGRMPWIWKDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKI
|
||||
AIVKLFKKYKLVKLPSVMKYGYKVKLEPRNQ
|
||||
|
||||
>seq0017
|
||||
FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKH
|
||||
LKIINEFASNIIHKKRQQFYDLISLFMITDEELRDIALNFIIAGRDTTAQLLSWFSYLVT
|
||||
ENESVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDIKLPHIIR
|
||||
KGDGIVIPTFAMGRMPWIWSNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIA
|
||||
IIKLFKKYKLEAVPSVMKYGFNVKLVPRKQET
|
||||
|
||||
>seq0018
|
||||
NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERKFDLLSL
|
||||
FLTSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQECEAKVTKEIMEHVPTYEMVKC
|
||||
QYLENALLETLRLRPSVPHLVRFAKVDILLPHVIRKGDGIVVPTYAMGRMPSLWKDPLKF
|
||||
DPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFKLEPLSSIMKNGFRVKL
|
||||
VPR
|
||||
|
||||
>seq0019
|
||||
KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDL
|
||||
YNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQYKD
|
||||
LLTLYFATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHAHVDARILEEIHTYVGTYQ
|
||||
MVKLKYMESCFLETLRLHPSVPHLVRFALVDIKLPHVIRKGDGVVVPVYAMGRMPWLWPK
|
||||
PLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYRIVARESIMKDGF
|
||||
YARLQPRAQQQQ
|
||||
|
||||
>seq0020
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
|
||||
FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
|
||||
KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
|
||||
VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
|
||||
VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>seq0021
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
|
||||
FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
|
||||
KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
|
||||
VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
|
||||
VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>seq0022
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
|
||||
FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
|
||||
KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
|
||||
VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
|
||||
VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>seq0023
|
||||
MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
|
||||
LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
|
||||
FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
|
||||
PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
|
||||
ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>seq0024
|
||||
MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
|
||||
LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
|
||||
FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
|
||||
PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
|
||||
ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>seq0026
|
||||
PFFGHNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYM
|
||||
FEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWREL
|
||||
HIHTAIIEQQISEVIQRNVNYDLLSLFLASENELRDVAMNFIIAGRDTTAQLLSWFSYLL
|
||||
TNPKVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDIPLLNIIR
|
||||
KGDCIIIPTYAMGRMPWLWNNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIV
|
||||
IIKLLRKYRIVAIPSVMKNGFKVRLELR
|
||||
|
||||
>seq0027
|
||||
ITMNFIIAGKDTTAQLLSWFFYVITHNRSDEVISNILNEFDAQSNGYEKMKLQYLEYCLL
|
||||
ETLRLFPSVPHLIRFAKSDIFRVDYTIRKGDGIVIPLYAMGRMPWIWENPDEFDPLRFQF
|
||||
LPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYRFVTQESPMKNGYKVKLIPK
|
||||
|
||||
>seq0028
|
||||
LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDL
|
||||
YDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERLCD
|
||||
LLSLFIITDVELRDITINFVIAGRDTTAQLLSWFSYLITWPQVEKKVLKEIKEVFPDYGK
|
||||
IKLEYLENAFLETLRMHPSVPHLVREAKVDIHLPHIIRKGDGVIVPTYAMGRLPWLWEKP
|
||||
EEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYKFEPLPSAMKNGFK
|
||||
VKLVPRDTQ
|
||||
|
||||
>seq0029
|
||||
LRDVAMNFIIAGRDTTAQLLSWFMYLFTNKEIEKPILNEINSIINYIDVKLKYLENCFFE
|
||||
TLRLRPAVPHLLRFAKTDIQLKYVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSP
|
||||
SKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
|
||||
|
||||
>seq0030
|
||||
YVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLE
|
||||
AKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
|
||||
|
||||
>seq0031
|
||||
IKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDA
|
||||
LKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFR
|
||||
VKLIKRQT
|
||||
|
||||
>seq0032
|
||||
NQHVEDKIMDEINQHINYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKD
|
||||
DTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIV
|
||||
KLFKKYKFIPIESLMKNGFRVKLIKRQTQF
|
||||
|
||||
>seq0033
|
||||
RVRAAQLLSWFLYEITENNEILSNINNEINEYINYDNIKLVYLENCFLETLRLRPSVPHL
|
||||
VRQANVDINIPYTIRKDDTIIVPTYAMGRMDYIWENPLKFDPNRFKHSPSKYPAFNIKPR
|
||||
LCLGKHVALLEAKIAIAKLFQKYKFEPIKSVMKNGFKVKVVPNIFK
|
||||
|
||||
>seq0034
|
||||
SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDIPIPYTIRKDDTIIVPTYA
|
||||
MGRMDYIWENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYKFE
|
||||
PIKSVMKNGFKVKVVPIE
|
||||
|
||||
>seq0035
|
||||
PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
|
||||
FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
|
||||
KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
|
||||
ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
|
||||
IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
|
||||
IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
|
||||
|
||||
>seq0036
|
||||
PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
|
||||
FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
|
||||
KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
|
||||
ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
|
||||
IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
|
||||
IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
|
||||
|
||||
>seq0037
|
||||
KQVQYDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFTYELCPHVYDQIMKEIDQVI
|
||||
GTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDFRLPHIIRKGDGIVCAAYLMGHISH
|
||||
LWDDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFKIIPVPAPM
|
||||
KNGFKVTLHNIETD
|
||||
|
||||
>seq0038
|
||||
YDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFIYELSPHVQDQIMNEINHVIGDYH
|
||||
LIKLKYLENALLETLRLHPAVPHLLRFATRDFRIPHIIRKGDGIVCAAYIMGHVPELWNN
|
||||
PHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFKIIPVPAPMKNGF
|
||||
KVTLECRN
|
||||
|
||||
>seq0039
|
||||
IRYDLLSLFLITEKELRDIAMNFIIAGRDTTAQTLSWFIYELTSPDVEENILKEIDSIGT
|
||||
YENIKFKYLENALLETLRMHPAVPHLVRYATRDILLRNIVRKGDGIVVGAYVMGHIPWLW
|
||||
PDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYRIEAIKAPMRY
|
||||
GFKVKLHPRL
|
||||
|
||||
>seq0041
|
||||
YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
|
||||
YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
|
||||
KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
|
||||
AG
|
||||
|
||||
>seq0042
|
||||
YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
|
||||
YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
|
||||
KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
|
||||
AGFQAHLQK
|
||||
|
||||
>seq0043
|
||||
KVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKD
|
||||
PLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG
|
||||
FQAHLQK
|
||||
|
||||
>seq0044
|
||||
EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDIKLPYTVRPGDEVFVSAYAMGRMPWV
|
||||
WEDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPM
|
||||
GAGFQAHLQK
|
||||
|
||||
>seq0045
|
||||
FDLISMFIITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHKLQQVMDNIRAEIRRVFGD
|
||||
YEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDIATHYVIRKGDEVMVAAYSMARMPWLW
|
||||
DDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPME
|
||||
TGFKAHLNVR
|
||||
|
||||
>seq0046
|
||||
INFIIAGKDTTAQMLSWFFYHINNLYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLR
|
||||
LYPSVPHLVRTAVKDIRTPYVIRKGDEIFISAWSMGRAPWIWDEPLQFKPERFMIDPSRF
|
||||
PAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE
|
||||
|
||||
>seq0047
|
||||
PFVGHHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYM
|
||||
FDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEM
|
||||
RSHIDWIEDYIYKVIANRRAYYYDLLSMFLISDKELRDITVNFIIAGKDTTAQMLSWFTY
|
||||
HLHKLIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDIETYY
|
||||
TIRAGDEVLICPLSMSRLEWIWPNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEG
|
||||
KIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP
|
||||
|
||||
>seq0048
|
||||
IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSM
|
||||
GRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQ
|
||||
AFQSAMKNGLKVVLK
|
||||
|
||||
>seq0049
|
||||
IAGRDTTSQMLSWFMFHLTKNDGMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRL
|
||||
YPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYP
|
||||
AFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
|
||||
|
||||
>seq0050
|
||||
YDLLSMFIISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSDMKTIESNIRNEIKTIF
|
||||
GTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDIQTPYTIRKNDEIMISTYSIGRSKY
|
||||
IWKDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSA
|
||||
MKNGWKVTLE
|
||||
|
||||
>seq0051
|
||||
YDLLSMFIISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQNDGMSDIEKKIRNEIDNI
|
||||
FGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSK
|
||||
YIWDKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPS
|
||||
AMKNGWKLDLK
|
||||
|
||||
>seq0052
|
||||
MLSWFYFHLTQNDGMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLR
|
||||
TAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDDPLKFDANRFIYDASVYPAFNIQPRLC
|
||||
LGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK
|
||||
|
||||
>seq0053
|
||||
VECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWEN
|
||||
ADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM
|
||||
|
||||
>seq0054
|
||||
IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGD
|
||||
EIIITTFPLGRLPWLWGNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVA
|
||||
MFTNFKSFQAVPAAMDGGFKIHIH
|
||||
|
||||
>seq0055
|
||||
IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDFKLKIYTFYKGD
|
||||
EIVVTTFAMGRLPWLWKNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIA
|
||||
MFSQFKSFRTVPAAMDGGFNIYVE
|
||||
|
||||
>seq0056
|
||||
IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLR
|
||||
LYPSVPHFVRQMVTDLTLNIYTFEKGDEIVVFTIALGKLPWLWENADEFIPERFIYDAEI
|
||||
WPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD
|
||||
|
||||
>seq0057
|
||||
YDLLSIFIINDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVD
|
||||
VFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDLTLNIYTFHKGDEVIVCTIALGK
|
||||
LPWLWENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTV
|
||||
PAPFRNGFNIYLK
|
||||
|
||||
>seq0058
|
||||
DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEA
|
||||
CLKETLRMYPSVPHFVREMVTDMKINIYIFEKGNEIIICTIALGKLPWLWDNANEFIPER
|
||||
FIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP
|
||||
|
||||
>seq0059
|
||||
LLSWFLYLVYENGKKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERT
|
||||
AVEDIKLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAP
|
||||
RICLGKHVALLEAKLVVIKLLRHFTIQPVKSAMKNGYKIILKRR
|
||||
|
||||
>seq0061
|
||||
ERIESHDLLSLFMFTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNPHVLQLVIDEIN
|
||||
TLTYDNVELTYLESALLETQRLHPSVPTLNRQAKRDIKLPFTVKKGDIYMVHNYAMGRAP
|
||||
WIWEDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME
|
||||
|
||||
>seq0062
|
||||
YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHPDIVDQIRNEINQVTY
|
||||
ESLEMKYTESALLETQRLHPSVPSLIRFAFQDIVLPYTIRKGDAVNVFNYAMGRSPWIWE
|
||||
NPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFNFKAVPAPLKNG
|
||||
FQVHLQPLHPTQN
|
||||
|
||||
@ -1,366 +0,0 @@
|
||||
>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_17829_Len879_Cov11_OG5_126554
|
||||
ISFDASVFKWGELAAHMKVVDGFADEMIAKCRYDLLSKFIISTRELRDILLNFIIAGRDT
|
||||
TAQLLSWCSYELCRNPEIQSKIYDELKTYQTVKMKYLEAVLYESLRLHPSVPNMTRFATR
|
||||
DIQLNNTIRKGDAVLVSNYVLGRLQKWWDNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKH
|
||||
VAMMEAKIGLATILKDYRMELKPGPMKNGCYINFIDRLSE
|
||||
|
||||
>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_9262_Len672_Cov8_OG5_126554
|
||||
YDLLTKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNPEIQDKVYEELSTYQSV
|
||||
KMKYLEAVLYEALRLHPSVPNMSRFATRDIQLSDVIRKGDCILVSNYVLGRLHQWWENAL
|
||||
QFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYRMELKPGPMKNGCFI
|
||||
NFIDRSTK
|
||||
|
||||
>Sr_rh_Al01_XX_Sr_rh_Al01-LKH192_6022_Len1275_Cov17_OG5_126554
|
||||
IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKC
|
||||
ELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTII
|
||||
QKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMRE
|
||||
IEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAM
|
||||
GRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEA
|
||||
VPSVMKYGFKVKLIPR
|
||||
|
||||
>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_11955_Len555_Cov4_OG5_126554
|
||||
LLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAK
|
||||
VDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGK
|
||||
HVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVNLIPR
|
||||
|
||||
>Sr_rh_HgpA_XX_Sr_rh_HgpA-LKH314_3374_Len948_Cov16_OG5_126554
|
||||
ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAG
|
||||
RDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPH
|
||||
LIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPP
|
||||
RLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
|
||||
|
||||
>Sr_rh_Nn01_XX_Sr_rh_Nn01_Contig_13892_Len1674_Cov284_OG5_126554
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
|
||||
FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
|
||||
KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
|
||||
LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
|
||||
IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
|
||||
|
||||
>Sr_rh_Nn02_XX_Sr_rh_Nn02_Contig_13025_Len1674_Cov94_OG5_126554
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
|
||||
FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
|
||||
KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
|
||||
LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
|
||||
IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
|
||||
|
||||
>Sr_rh_Nn10_XX_Sr_rh_Nn10_Contig_21569_Len1563_Cov139_OG5_126554
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
|
||||
FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
|
||||
KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
|
||||
LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
|
||||
IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPR
|
||||
|
||||
>Sr_rh_Emac_XX_Sr_rh_Emac_Contig_11467_Len1551_Cov70_OG5_126554
|
||||
PYFGHHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYM
|
||||
FQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTL
|
||||
KAHVKVINEFAERIIRSKRKDYYDIMSLFLISDQELRDMALNFIIAGRDTTAQLLSWFSY
|
||||
AMTENADVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDIDLPE
|
||||
TIRKGNGIVIPTFAMGRMPWIWKDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAVVKLFTKYKLVPMPSVMKNGFKVKLIPRE
|
||||
|
||||
>Sr_rh_Al02_XX_Sr_rh_Al02-LKH279_3746_Len555_Cov10_OG5_126554
|
||||
LMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAK
|
||||
VDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGK
|
||||
HVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
|
||||
|
||||
>Sr_rh_As04_XX_Sr_rh_As04-LKH296_1295_Len732_Cov6_OG5_126554
|
||||
YDLMSLFLISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENEEVEKKIVEEIRLYVGD
|
||||
YNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIW
|
||||
KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKN
|
||||
GLKVRLIPRGK
|
||||
|
||||
>Sr_rh_As01_XX_Sr_rh_As01-LKH294_6033_Len771_Cov5_OG5_126554
|
||||
YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
|
||||
YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
|
||||
KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
|
||||
GFKVRLVPRCK
|
||||
|
||||
>Sr_rh_As05_XX_Sr_rh_As05-LKH295_5839_Len819_Cov11_OG5_126554
|
||||
RSSSKKQHFYDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIM
|
||||
QEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTY
|
||||
AMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKL
|
||||
DALPSVMKNGFKVRLVPRCK
|
||||
|
||||
>Sr_rh_As03_XX_Sr_rh_As03-LKH313_6888_Len702_Cov8_OG5_126554
|
||||
YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
|
||||
YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
|
||||
KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
|
||||
GFKVRLVPRCK
|
||||
|
||||
>Sr_rh_As02_XX_Sr_rh_As02-LKH324_15814_Len489_Cov16_OG5_126554
|
||||
MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDIPLPDVIRKGDGVIVPMYAM
|
||||
GRMPWLWKNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFKLEA
|
||||
LPTVMKNGFKVKLIPRCK
|
||||
|
||||
>Sr_rh_Ts02_XX_Sr_rh_Ts02-LKH320_6145_Len708_Cov5_OG5_126554
|
||||
YDLMSLFLITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNKQIEENIMNEINQYIGD
|
||||
YNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDIKLPDIIRKGDGIVIPTYAMGRMPWIW
|
||||
NDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLQPLPSIMRN
|
||||
GFKVKLIPRDSK
|
||||
|
||||
>Sr_rh_Calb_XX_Contig_7745_Len1683_Cov38_OG5_126554
|
||||
PLIGHNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYM
|
||||
FNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSL
|
||||
KKHSHILNDFAKKVIDDRKSYDLLSLFLVNVSELRDVCINFIVAGRDTTAQLLSWFMYEL
|
||||
SNPKIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDIELPGHII
|
||||
RKGDGIVIPTYAMGRMPWIWKDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKI
|
||||
AIVKLFKKYKLVKLPSVMKYGYKVKLEPRNQ
|
||||
|
||||
>Sr_rh_RspA_XX_Sr_rh_RspA-LKH290_4671_Len1062_Cov25_OG5_126554
|
||||
FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKH
|
||||
LKIINEFASNIIHKKRQQFYDLISLFMITDEELRDIALNFIIAGRDTTAQLLSWFSYLVT
|
||||
ENESVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDIKLPHIIR
|
||||
KGDGIVIPTFAMGRMPWIWSNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIA
|
||||
IIKLFKKYKLEAVPSVMKYGFNVKLVPRKQET
|
||||
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_1649_Len957_Cov10_OG5_126554
|
||||
NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERKFDLLSL
|
||||
FLTSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQECEAKVTKEIMEHVPTYEMVKC
|
||||
QYLENALLETLRLRPSVPHLVRFAKVDILLPHVIRKGDGIVVPTYAMGRMPSLWKDPLKF
|
||||
DPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFKLEPLSSIMKNGFRVKL
|
||||
VPR
|
||||
|
||||
>Sr_rh_Hind_XX_Contig_12080_Len1260_Cov53_OG5_126554
|
||||
KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDL
|
||||
YNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQYKD
|
||||
LLTLYFATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHAHVDARILEEIHTYVGTYQ
|
||||
MVKLKYMESCFLETLRLHPSVPHLVRFALVDIKLPHVIRKGDGVVVPVYAMGRMPWLWPK
|
||||
PLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYRIVARESIMKDGF
|
||||
YARLQPRAQQQQ
|
||||
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20076_Len1179_Cov40_OG5_126554
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
|
||||
FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
|
||||
KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
|
||||
VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
|
||||
VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19982_Len1182_Cov79_OG5_126554
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
|
||||
FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
|
||||
KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
|
||||
VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
|
||||
VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_20382_Len1167_Cov94_OG5_126554
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
|
||||
FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
|
||||
KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
|
||||
VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
|
||||
VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19888_Len1155_Cov80_OG5_126554
|
||||
MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
|
||||
LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
|
||||
FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
|
||||
PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
|
||||
ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>Sr_rh_Tx01_XX_Sr_rh_Tx01_Contig_19044_Len1188_Cov38_OG5_126554
|
||||
MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
|
||||
LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
|
||||
FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
|
||||
PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
|
||||
ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>Sr_rh_Slin_XX_Contig_3275_Len1587_Cov14_OG5_126554
|
||||
PFFGHNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYM
|
||||
FEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWREL
|
||||
HIHTAIIEQQISEVIQRNVNYDLLSLFLASENELRDVAMNFIIAGRDTTAQLLSWFSYLL
|
||||
TNPKVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDIPLLNIIR
|
||||
KGDCIIIPTYAMGRMPWLWNNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIV
|
||||
IIKLLRKYRIVAIPSVMKNGFKVRLELR
|
||||
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_3920_Len636_Cov5_OG5_126554
|
||||
ITMNFIIAGKDTTAQLLSWFFYVITHNRSDEVISNILNEFDAQSNGYEKMKLQYLEYCLL
|
||||
ETLRLFPSVPHLIRFAKSDIFRVDYTIRKGDGIVIPLYAMGRMPWIWENPDEFDPLRFQF
|
||||
LPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYRFVTQESPMKNGYKVKLIPK
|
||||
|
||||
>Sr_rh_PspA_XX_Sr_rh_PspA-LKH285_926_Len1191_Cov12_OG5_126554
|
||||
LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDL
|
||||
YDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERLCD
|
||||
LLSLFIITDVELRDITINFVIAGRDTTAQLLSWFSYLITWPQVEKKVLKEIKEVFPDYGK
|
||||
IKLEYLENAFLETLRMHPSVPHLVREAKVDIHLPHIIRKGDGVIVPTYAMGRLPWLWEKP
|
||||
EEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYKFEPLPSAMKNGFK
|
||||
VKLVPRDTQ
|
||||
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_3536_Len591_Cov9_OG5_126554
|
||||
LRDVAMNFIIAGRDTTAQLLSWFMYLFTNKEIEKPILNEINSIINYIDVKLKYLENCFFE
|
||||
TLRLRPAVPHLLRFAKTDIQLKYVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSP
|
||||
SKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
|
||||
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_14775_Len321_Cov15_OG5_126554
|
||||
YVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLE
|
||||
AKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
|
||||
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_8241_Len441_Cov6_OG5_126554
|
||||
IKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDA
|
||||
LKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFR
|
||||
VKLIKRQT
|
||||
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_5955_Len525_Cov17_OG5_126554
|
||||
NQHVEDKIMDEINQHINYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKD
|
||||
DTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIV
|
||||
KLFKKYKFIPIESLMKNGFRVKLIKRQTQF
|
||||
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6707_Len579_Cov20_OG5_126554
|
||||
RVRAAQLLSWFLYEITENNEILSNINNEINEYINYDNIKLVYLENCFLETLRLRPSVPHL
|
||||
VRQANVDINIPYTIRKDDTIIVPTYAMGRMDYIWENPLKFDPNRFKHSPSKYPAFNIKPR
|
||||
LCLGKHVALLEAKIAIAKLFQKYKFEPIKSVMKNGFKVKVVPNIFK
|
||||
|
||||
>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_9807_Len483_Cov16_OG5_126554
|
||||
SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDIPIPYTIRKDDTIIVPTYA
|
||||
MGRMDYIWENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYKFE
|
||||
PIKSVMKNGFKVKVVPIE
|
||||
|
||||
>Sr_rh_Bv04_XX_Sr_rh_Bv04_Contig_12687_Len1599_Cov64_OG5_126554
|
||||
PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
|
||||
FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
|
||||
KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
|
||||
ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
|
||||
IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
|
||||
IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
|
||||
|
||||
>Sr_rh_Bv05_XX_Sr_rh_Bv05_Contig_10933_Len1599_Cov61_OG5_126554
|
||||
PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
|
||||
FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
|
||||
KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
|
||||
ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
|
||||
IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
|
||||
IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
|
||||
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_10605_Len690_Cov15_OG5_126554
|
||||
KQVQYDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFTYELCPHVYDQIMKEIDQVI
|
||||
GTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDFRLPHIIRKGDGIVCAAYLMGHISH
|
||||
LWDDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFKIIPVPAPM
|
||||
KNGFKVTLHNIETD
|
||||
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_18259_Len648_Cov21_OG5_126554
|
||||
YDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFIYELSPHVQDQIMNEINHVIGDYH
|
||||
LIKLKYLENALLETLRLHPAVPHLLRFATRDFRIPHIIRKGDGIVCAAYIMGHVPELWNN
|
||||
PHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFKIIPVPAPMKNGF
|
||||
KVTLECRN
|
||||
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13702_Len678_Cov20_OG5_126554
|
||||
IRYDLLSLFLITEKELRDIAMNFIIAGRDTTAQTLSWFIYELTSPDVEENILKEIDSIGT
|
||||
YENIKFKYLENALLETLRMHPAVPHLVRYATRDILLRNIVRKGDGIVVGAYVMGHIPWLW
|
||||
PDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYRIEAIKAPMRY
|
||||
GFKVKLHPRL
|
||||
|
||||
>Sr_rh_As01_XX_Sr_rh_As01-LKH294_2597_Len693_Cov4_OG5_126554
|
||||
YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
|
||||
YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
|
||||
KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
|
||||
AG
|
||||
|
||||
>Sr_rh_As03_XX_Sr_rh_As03-LKH313_10378_Len717_Cov12_OG5_126554
|
||||
YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
|
||||
YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
|
||||
KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
|
||||
AGFQAHLQK
|
||||
|
||||
>Sr_rh_As05_XX_Sr_rh_As05-LKH295_19507_Len444_Cov9_OG5_126554
|
||||
KVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKD
|
||||
PLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG
|
||||
FQAHLQK
|
||||
|
||||
>Sr_rh_As02_XX_Sr_rh_As02-LKH324_14147_Len456_Cov8_OG5_126554
|
||||
EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDIKLPYTVRPGDEVFVSAYAMGRMPWV
|
||||
WEDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPM
|
||||
GAGFQAHLQK
|
||||
|
||||
>Sr_rh_Emar_XX_Contig_8285_Len723_Cov12_OG5_126554
|
||||
FDLISMFIITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHKLQQVMDNIRAEIRRVFGD
|
||||
YEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDIATHYVIRKGDEVMVAAYSMARMPWLW
|
||||
DDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPME
|
||||
TGFKAHLNVR
|
||||
|
||||
>Sr_rh_Hg01_XX_Sr_rh_Hg01-LKH304_7769_Len600_Cov7_OG5_126554
|
||||
INFIIAGKDTTAQMLSWFFYHINNLYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLR
|
||||
LYPSVPHLVRTAVKDIRTPYVIRKGDEIFISAWSMGRAPWIWDEPLQFKPERFMIDPSRF
|
||||
PAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE
|
||||
|
||||
>Sr_rh_Hind_XX_Contig_2010_Len1647_Cov26_OG5_126554
|
||||
PFVGHHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYM
|
||||
FDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEM
|
||||
RSHIDWIEDYIYKVIANRRAYYYDLLSMFLISDKELRDITVNFIIAGKDTTAQMLSWFTY
|
||||
HLHKLIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDIETYY
|
||||
TIRAGDEVLICPLSMSRLEWIWPNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEG
|
||||
KIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP
|
||||
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_6436_Len489_Cov15_OG5_126554
|
||||
IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSM
|
||||
GRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQ
|
||||
AFQSAMKNGLKVVLK
|
||||
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6395_Len597_Cov13_OG5_126554
|
||||
IAGRDTTSQMLSWFMFHLTKNDGMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRL
|
||||
YPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYP
|
||||
AFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
|
||||
|
||||
>Sr_rh_Sspa_XX_Contig_5747_Len702_Cov21_OG5_126554
|
||||
YDLLSMFIISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSDMKTIESNIRNEIKTIF
|
||||
GTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDIQTPYTIRKNDEIMISTYSIGRSKY
|
||||
IWKDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSA
|
||||
MKNGWKVTLE
|
||||
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_256_Len708_Cov14_OG5_126554
|
||||
YDLLSMFIISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQNDGMSDIEKKIRNEIDNI
|
||||
FGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSK
|
||||
YIWDKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPS
|
||||
AMKNGWKLDLK
|
||||
|
||||
>Sr_rh_QjpA_XX_Sr_rh_QjpA-LKH288_9889_Len564_Cov19_OG5_126554
|
||||
MLSWFYFHLTQNDGMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLR
|
||||
TAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDDPLKFDANRFIYDASVYPAFNIQPRLC
|
||||
LGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK
|
||||
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_13181_Len408_Cov3_OG5_126554
|
||||
VECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWEN
|
||||
ADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM
|
||||
|
||||
>Sr_rh_Mf03_XX_Sr_rh_Mf03-LKH281_6167_Len516_Cov7_OG5_126554
|
||||
IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGD
|
||||
EIIITTFPLGRLPWLWGNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVA
|
||||
MFTNFKSFQAVPAAMDGGFKIHIH
|
||||
|
||||
>Sr_rh_Mf02_XX_Sr_rh_Mf02-LKH282_190_Len516_Cov4_OG5_126554
|
||||
IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDFKLKIYTFYKGD
|
||||
EIVVTTFAMGRLPWLWKNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIA
|
||||
MFSQFKSFRTVPAAMDGGFNIYVE
|
||||
|
||||
>Sr_rh_Qj01_XX_Sr_rh_Qj01-LKH287_6601_Len603_Cov10_OG5_126554
|
||||
IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLR
|
||||
LYPSVPHFVRQMVTDLTLNIYTFEKGDEIVVFTIALGKLPWLWENADEFIPERFIYDAEI
|
||||
WPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD
|
||||
|
||||
>Sr_rh_Tr01_XX_Sr_rh_Tr01_Contig_5346_Len690_Cov14_OG5_126554
|
||||
YDLLSIFIINDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVD
|
||||
VFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDLTLNIYTFHKGDEVIVCTIALGK
|
||||
LPWLWENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTV
|
||||
PAPFRNGFNIYLK
|
||||
|
||||
>Sr_rh_Tr02_XX_Sr_rh_Tr02_Contig_17503_Len567_Cov70_OG5_126554
|
||||
DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEA
|
||||
CLKETLRMYPSVPHFVREMVTDMKINIYIFEKGNEIIICTIALGKLPWLWDNANEFIPER
|
||||
FIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP
|
||||
|
||||
>Sr_rh_FF02_XX_Sr_rh_FF02_Contig_5686_Len600_Cov5_OG5_126554
|
||||
LLSWFLYLVYENGKKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERT
|
||||
AVEDIKLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAP
|
||||
RICLGKHVALLEAKLVVIKLLRHFTIQPVKSAMKNGYKIILKRR
|
||||
|
||||
>Sr_rh_Pfue_XX_Sr_rh_Pfue_Contig_20190_Len552_Cov3_OG5_126554
|
||||
ERIESHDLLSLFMFTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNPHVLQLVIDEIN
|
||||
TLTYDNVELTYLESALLETQRLHPSVPTLNRQAKRDIKLPFTVKKGDIYMVHNYAMGRAP
|
||||
WIWEDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME
|
||||
|
||||
>Sr_rh_Ti04_XX_Sr_rh_Ti04-LKH210_13699_Len690_Cov51_OG5_126554
|
||||
YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHPDIVDQIRNEINQVTY
|
||||
ESLEMKYTESALLETQRLHPSVPSLIRFAFQDIVLPYTIRKGDAVNVFNYAMGRSPWIWE
|
||||
NPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFNFKAVPAPLKNG
|
||||
FQVHLQPLHPTQN
|
||||
|
||||
@ -1,386 +0,0 @@
|
||||
>seq0000
|
||||
ISFDASVFKWGELAAHMKVVDGFADEMIAKCRYDLLSKFIISTRELRDILLNFIIAGRDT
|
||||
TAQLLSWCSYELCRNPEIQSKIYDELKTYQTVKMKYLEAVLYESLRLHPSVPNMTRFATR
|
||||
DIQLNNTIRKGDAVLVSNYVLGRLQKWWDNPYKFDPMRFYYKAHEYTNFNIPPRLCLGKH
|
||||
VAMMEAKIGLATILKDYRMELKPGPMKNGCYINFIDRLSE
|
||||
|
||||
>seq0001
|
||||
YDLLTKFIISTRELRDILLNFIIAGRDTTAQLLSWCSYELCLNPEIQDKVYEELSTYQSV
|
||||
KMKYLEAVLYEALRLHPSVPNMSRFATRDIQLSDVIRKGDCILVSNYVLGRLHQWWENAL
|
||||
QFDPMRFYYKAHEYTNFNVPPRLCLGKHVALMEAKIALATVLKDYRMELKPGPMKNGCFI
|
||||
NFIDRSTK
|
||||
|
||||
>seq0002
|
||||
IDLLFDADKSPVLGKGIFVADGNIWKKHRAIASRMFTVRSLRDYMFEVFMDTTDAFIDKC
|
||||
ELYTQCVDIYDMYNRLTLEAFTMVAFGVPLGVISFDDGQTRVRTLKKHEQIINEFANTII
|
||||
QKKRKHFYDIMSLFLVSDAELRDVALNFIVAGRDTTAQLLSWFSYAMSENKGVEEKIMRE
|
||||
IEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAKVDIELPDVIRKGDAIIIPTFAM
|
||||
GRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGKHVALMEAKIAIIKLFKKYKLEA
|
||||
VPSVMKYGFKVKLIPR
|
||||
|
||||
>seq0003
|
||||
LLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPHLIRYAK
|
||||
VDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPPRLCLGK
|
||||
HVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVNLIPR
|
||||
|
||||
>seq0004
|
||||
ISFDDGQTRVRTLKKHVQIINEFANTIIQKKRKHFYDIMSLFLVSDAELRDVALNFIVAG
|
||||
RDTTAQLLSWFSYAMSENKGVEEKIMREIEQHIGNYNSIQCKYLENALLESLRLRPSVPH
|
||||
LIRYAKVDIELPDVIRKGDAIIIPTFAMGRMPWIWKDPLKFNPDRFNFTPSQYPAFNIPP
|
||||
RLCLGKHVALMEAKIAIIKLFKKYKLEAVPSVMKYGFKVKLIPR
|
||||
|
||||
>seq0005
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
|
||||
FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
|
||||
KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
|
||||
LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
|
||||
IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
|
||||
|
||||
>seq0006
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
|
||||
FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
|
||||
KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
|
||||
LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
|
||||
IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPRES
|
||||
|
||||
>seq0007
|
||||
PYFGHNFIFVVDPKIVDLLFNADKRPILGKGIFISDGNIWKKHRAIASRMFTVRSLRDYM
|
||||
FEVFNDTTDTFVAKCEICTTCVDMYDMYNRLTLEAFTMVAFGVQLGVISFDAAQTKARTL
|
||||
KKHINIINEFANEFIQKKREHLYDIMWLFLISDEELRDIALNFIIAGRDTTAQLLSWCTY
|
||||
LLSENQHVYRKIMQEMDQHIGDFNAIHCKYLEKCFLESLRLRPSVPHLVRYAKVDIALPD
|
||||
IIRKGDGIVVPTFAMGRMPWIWKDPLKFNPDRFNYTPSQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAIIKLFKKYKLEPVSSVMKNGFKVKLIPR
|
||||
|
||||
>seq0008
|
||||
PYFGHHFIFVVDPALIDLLFDADKRPILGRGIFTSDGLLWKKHRSIASRMFTVRSLRDYM
|
||||
FQVFRDTTDTFMSKCEICANHVDIYDMFHRLTLEAFTQVAFGVSLGVIAFDDAQTKARTL
|
||||
KAHVKVINEFAERIIRSKRKDYYDIMSLFLISDQELRDMALNFIIAGRDTTAQLLSWFSY
|
||||
AMTENADVESKLLAELRQAVADYDAIDCTYLENALLESLRLRPSVPHLVRYAKVDIDLPE
|
||||
TIRKGNGIVIPTFAMGRMPWIWKDPLKFDPDRFNYTASQYPAFNIPPRLCLGKHVALLEA
|
||||
KIAVVKLFTKYKLVPMPSVMKNGFKVKLIPRE
|
||||
|
||||
>seq0009
|
||||
LMSWFSYAMTENEEVEKKIVEEIRLYVGDYNTINCQYLENAFLESLRMRPVLPHLVRYAK
|
||||
VDIALPHVIRKGDGLIVPSFAMGRMPWIWKDPNTFNPDRFKYTPAQYPAFNIPPRLCLGK
|
||||
HVALLEAKIMIIKLFKKYKLEAVPNIMKNGLKVRLIPRGK
|
||||
|
||||
>seq0010
|
||||
YDLMSLFLISDDELRDVALNFILAGRDTTAQLMSWFSYAMTENEEVEKKIVEEIRLYVGD
|
||||
YNTINCQYLENAFLESLRMRPVLPHLVRYAKVDIALPHVIRKGDGLIVPSFAMGRMPWIW
|
||||
KDPNTFNPDRFKYTPAQYPAFNIPPRLCLGKHVALLEAKIMIIKLFKKYKLEAVPNIMKN
|
||||
GLKVRLIPRGK
|
||||
|
||||
>seq0011
|
||||
YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
|
||||
YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
|
||||
KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
|
||||
GFKVRLVPRCK
|
||||
|
||||
>seq0012
|
||||
RSSSKKQHFYDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIM
|
||||
QEMQQFIGDYNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTY
|
||||
AMGRMPWIWKDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKL
|
||||
DALPSVMKNGFKVRLVPRCK
|
||||
|
||||
>seq0013
|
||||
YDLMSLFLVSDDELRDVALNFIIAGRDTTAQLLSWFSYAITENEEVEGKIMQEMQQFIGD
|
||||
YNNVNCQYLESAFLESLRLRPSVPHLVRYAKVDITLPDVVRKGDGIIIPTYAMGRMPWIW
|
||||
KDPLKFDPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLEALPSVMKN
|
||||
GFKVRLVPRCK
|
||||
|
||||
>seq0014
|
||||
MNQFIGNYDMLNCQYLESSFYESLRLQPSLPHLVRYAKVDIPLPDVIRKGDGVIVPMYAM
|
||||
GRMPWLWKNPDKFDPERFNYTPAEYPAFNIPPRVCLGKHVALMEAKIAVIKLLKKFKLEA
|
||||
LPTVMKNGFKVKLIPRCK
|
||||
|
||||
>seq0015
|
||||
YDLMSLFLITDDELRDIALNFIIAGRDTTAQLLSWFSYCITDNKQIEENIMNEINQYIGD
|
||||
YNVIQCEYLESSFLETLRLRPSVPHLVRYAKIDIKLPDIIRKGDGIVIPTYAMGRMPWIW
|
||||
NDPLKFNPDRFNYSPSQYPAFNIPPRLCLGKHVALLEAKIAIIKLFKKYKLQPLPSIMRN
|
||||
GFKVKLIPRDSK
|
||||
|
||||
>seq0016
|
||||
PLIGHNFIFMVSPKLIDLLFDSNKLPILGHGIFNADGQLWKKHRSIASRMFTVRSLRDYM
|
||||
FNVFVDTTDKWILKSEILKNFVDIYNMNLRLTMEAFTKVAFGVDLGTIAMDDGITKLKSL
|
||||
KKHSHILNDFAKKVIDDRKSYDLLSLFLVNVSELRDVCINFIVAGRDTTAQLLSWFMYEL
|
||||
SNPKIEEKIMEEINEYIGEYKQIECEYLENCLLETLRLRPSVPHLVRYAKCDIELPGHII
|
||||
RKGDGIVIPTYAMGRMPWIWKDPLKFNPDRFKHPPSKYPAFNIPPRLCLGKHVALLEAKI
|
||||
AIVKLFKKYKLVKLPSVMKYGYKVKLEPRNQ
|
||||
|
||||
>seq0017
|
||||
FNDTTDDFIAKCEICEMSVNIYDMFHRLTLEAFTMVAFGVPLGVISFDEGRTKWRTLKKH
|
||||
LKIINEFASNIIHKKRQQFYDLISLFMITDEELRDIALNFIIAGRDTTAQLLSWFSYLVT
|
||||
ENESVESKIMNEINECVADYNMVKCEYLENAFLETLRLRPSVPHLVRYAKTDIKLPHIIR
|
||||
KGDGIVIPTFAMGRMPWIWSNPLEFNPDRFKFTPAEYPAFNLPPRLCLGKHVALLEAKIA
|
||||
IIKLFKKYKLEAVPSVMKYGFNVKLVPRKQET
|
||||
|
||||
>seq0018
|
||||
NMYNRLTLEAFTQVAFGVPLGCISFDRGQSKLRELRKHLKVVNEFVSKVIVERKFDLLSL
|
||||
FLTSDKELRDVAMNFIVAGRDTTAQLLSWFSYLISENQECEAKVTKEIMEHVPTYEMVKC
|
||||
QYLENALLETLRLRPSVPHLVRFAKVDILLPHVIRKGDGIVVPTYAMGRMPSLWKDPLKF
|
||||
DPSRFEYTPSEYPAFNIPPRLCLGKHVALLESKIAIIRLFRKFKLEPLSSIMKNGFRVKL
|
||||
VPR
|
||||
|
||||
>seq0019
|
||||
KPVFGVGILSTDGKLWKKYRSIGSRIFTVRSLRDFMYEVFDSTSSALVKKSLIQEQFVDL
|
||||
YNMFNRLTLEAFTHIAFGVSMKTIAFDRSQWDFKELKKHAGILNDKIGLLVRQRKEQYKD
|
||||
LLTLYFATDLELRDLIMNFVVAGRDTTAQLCSWFSYEISEHAHVDARILEEIHTYVGTYQ
|
||||
MVKLKYMESCFLETLRLHPSVPHLVRFALVDIKLPHVIRKGDGVVVPVYAMGRMPWLWPK
|
||||
PLVFDPMRFEYTPALFPAFNIPPRLCLGKHLALLEAKVVMVKILRKYRIVARESIMKDGF
|
||||
YARLQPRAQQQQ
|
||||
|
||||
>seq0020
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
|
||||
FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
|
||||
KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
|
||||
VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
|
||||
VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>seq0021
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
|
||||
FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
|
||||
KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
|
||||
VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
|
||||
VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>seq0022
|
||||
MFTVRALRDYMFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIIS
|
||||
FDRGQTRWRELKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAG
|
||||
KDTTAQLLSWFSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHL
|
||||
VRYAKVDIPLPHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPR
|
||||
VCLGKHVALLECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>seq0023
|
||||
MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
|
||||
LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
|
||||
FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
|
||||
PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
|
||||
ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>seq0024
|
||||
MFEVFVNTSNIFLDKCCLQTQYFDIYNMYNRLTLEAFAQVAFGMPLDIISFDRGQTRWRE
|
||||
LKTHEKIMDELVKKVVKRCKTYYGNYDLLSLFLASYKELKDVTMNFIMAGKDTTAQLLSW
|
||||
FSWSLTNPEVEQRIVDEIHTYVGDYQIVKCQYLENALLESLRLNPSVPHLVRYAKVDIPL
|
||||
PHVIRKGDGIVVPTYAMGRMAWLWPNPTKFDPTRFEFTPAVYPAFNLPPRVCLGKHVALL
|
||||
ECKIVMIKLLRRFRIVACESAMKHGFKVRFEPREESAK
|
||||
|
||||
>seq0025
|
||||
PFFGHNFIFLCDPKLIDLIFDAEKKPMLGHGIFLSDGARWKKQRSIASRMFTVRSLRDYM
|
||||
FEVFVDTSNTFIDKCLIQSEEIDIYDMFNRLTLEAFTEVAFGVSLNIMSFDRGQ
|
||||
|
||||
>seq0026
|
||||
PFFGHNFIFLCDPKLIDFVFDANKKPLLGHGIFVSDGAKWKKHRSIASHMFTVRSLREYM
|
||||
FEVFVDTSNTFLDKCLIQSKEIDIYNMFNRLTLEAFTKVAFGVSLNIISFDRGQTAWREL
|
||||
HIHTAIIEQQISEVIQRNVNYDLLSLFLASENELRDVAMNFIIAGRDTTAQLLSWFSYLL
|
||||
TNPKVEQMIVDEINANIGDYEMVKCQYLENAFLETLRLHPSVPHLVRYAKTDIPLLNIIR
|
||||
KGDCIIIPTYAMGRMPWLWNNALTFDPSRFEYSPAQYPAFNIPPRLCLGKHVALLEAKIV
|
||||
IIKLLRKYRIVAIPSVMKNGFKVRLELR
|
||||
|
||||
>seq0027
|
||||
ITMNFIIAGKDTTAQLLSWFFYVITHNRSDEVISNILNEFDAQSNGYEKMKLQYLEYCLL
|
||||
ETLRLFPSVPHLIRFAKSDIFRVDYTIRKGDGIVIPLYAMGRMPWIWENPDEFDPLRFQF
|
||||
LPSEYPAFNIPPRLCLGKHVALMEAKIAVIKLLKKYRFVTQESPMKNGYKVKLIPK
|
||||
|
||||
>seq0028
|
||||
LPILGRGIIASDGKIWKRHRKVASRMFTLSSLRDYMFEVFNSTTDTLMDKMLIHKDHVDL
|
||||
YDMYNRLTLEAFTEVAFGVKLGVISFDRGASKFKELLFHEKTINNMVWDLVHKCKERLCD
|
||||
LLSLFIITDVELRDITINFVIAGRDTTAQLLSWFSYLITWPQVEKKVLKEIKEVFPDYGK
|
||||
IKLEYLENAFLETLRMHPSVPHLVREAKVDIHLPHIIRKGDGVIVPTYAMGRLPWLWEKP
|
||||
EEMNPDRFQFTPSEYPAFNIPPRLCLGKHVSLMEAKIQIVKLLPKYKFEPLPSAMKNGFK
|
||||
VKLVPRDTQ
|
||||
|
||||
>seq0029
|
||||
LRDVAMNFIIAGRDTTAQLLSWFMYLFTNKEIEKPILNEINSIINYIDVKLKYLENCFFE
|
||||
TLRLRPAVPHLLRFAKTDIQLKYVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSP
|
||||
SKYVAFNIPPRLCLGKHVALLEAKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
|
||||
|
||||
>seq0030
|
||||
YVIRKGDGICIPTFAMNRMPWIWDNPFKFDPNRFDQSPSKYVAFNIPPRLCLGKHVALLE
|
||||
AKLLVLELLTRFKIEPVLSAMRNGFKVYFHPR
|
||||
|
||||
>seq0031
|
||||
IKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKDDTILVPTYAMGRMEWIWKDA
|
||||
LKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIVKLFKKYKFIPIESLMKNGFR
|
||||
VKLIKRQT
|
||||
|
||||
>seq0032
|
||||
NQHVEDKIMDEINQHINYNTIKLNYLENSFLETLRLRPSVPHLVRKAVVDIKIPHIIRKD
|
||||
DTILVPTYAMGRMEWIWKDALKFDPTRFEYSPSKYPAFNIKPRLCLGKHVALLEAKIAIV
|
||||
KLFKKYKFIPIESLMKNGFRVKLIKRQTQF
|
||||
|
||||
>seq0033
|
||||
RVRAAQLLSWFLYEITENNEILSNINNEINEYINYDNIKLVYLENCFLETLRLRPSVPHL
|
||||
VRQANVDINIPYTIRKDDTIIVPTYAMGRMDYIWENPLKFDPNRFKHSPSKYPAFNIKPR
|
||||
LCLGKHVALLEAKIAIAKLFQKYKFEPIKSVMKNGFKVKVVPNIFK
|
||||
|
||||
>seq0034
|
||||
SINAEYGNYDNIKLIYLENCFLETLRLRPSVPHLVRQANVDIPIPYTIRKDDTIIVPTYA
|
||||
MGRMDYIWENALTFDPNRFKYSPSKYPAFNIKPRLCLGKHVALLEAKIAIAKLFKKYKFE
|
||||
PIKSVMKNGFKVKVVPIE
|
||||
|
||||
>seq0035
|
||||
PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
|
||||
FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
|
||||
KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
|
||||
ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
|
||||
IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
|
||||
IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
|
||||
|
||||
>seq0036
|
||||
PFIGHNYLFISDVKLIDYIFDAEKEPLTGDGIFASDGKLWKHHRSTASKMFTLRSLKDYM
|
||||
FEIFNDSTDAFLDKITLNDRYINIYDMFHRLTLEAFTQAALGINLGVISFDFVHINYGEL
|
||||
KKHEEIINKKIQDIISKRKEQYDIISIFLISDKELRDICANFILAGRDTTGQLLSWFCYE
|
||||
ICENKHIVNKIIEEIDEHIGSYQQVKMEYLENALLECLRLRPSVPHLVRVAKTDILIPHV
|
||||
IRKGDTIIVPCYAMGRMPTIWKEPLKFDPLRFNFPPCKYPAFNIPPRLCLGKHVAIMEAK
|
||||
IAIVKLFRKYELIPDTSMMKTGFRVRLKSR
|
||||
|
||||
>seq0037
|
||||
KQVQYDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFTYELCPHVYDQIMKEIDQVI
|
||||
GTYDLIKLKYLENALLETLRLHPAVPHLLRFATRDFRLPHIIRKGDGIVCAAYLMGHISH
|
||||
LWDDPERFDPTRFEYDPSYFPAFNIAPRICLGKHVALLEAKIAAIKLFKKFKIIPVPAPM
|
||||
KNGFKVTLHNIETD
|
||||
|
||||
>seq0038
|
||||
YDLLSLFLMSIKELRDISMNFIIAGRDTTAQTLSWFIYELSPHVQDQIMNEINHVIGDYH
|
||||
LIKLKYLENALLETLRLHPAVPHLLRFATRDFRIPHIIRKGDGIVCAAYIMGHVPELWNN
|
||||
PHQFDPTRFEYDPSYFPAFNIAPRLCLGKHVALLEAKIAAVKLLKKFKIIPVPAPMKNGF
|
||||
KVTLECRN
|
||||
|
||||
>seq0039
|
||||
IRYDLLSLFLITEKELRDIAMNFIIAGRDTTAQTLSWFIYELTSPDVEENILKEIDSIGT
|
||||
YENIKFKYLENALLETLRMHPAVPHLVRYATRDILLRNIVRKGDGIVVGAYVMGHIPWLW
|
||||
PDPERFDPTRFEYDPCYFPVFNVAPRLCLGKHVALLEAKIAAVKLLKKYRIEAIKAPMRY
|
||||
GFKVKLHPRL
|
||||
|
||||
>seq0040
|
||||
PFIGHIKNFIFIVDPKIIDLLFDKRPMFGDGIFSSDGNIWKKHRALASRMFTLRSLRDYM
|
||||
FKSFCSTTDEFINKLSVDIYDMYNRLTLEAFTYVAFGTNLGAISQAPEELEFTSFDKICK
|
||||
RFFDPIKM
|
||||
|
||||
>seq0041
|
||||
YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
|
||||
YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
|
||||
KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
|
||||
AG
|
||||
|
||||
>seq0042
|
||||
YDLLSMFIITDQELRDITFSFIIAGKDTTAQMLSWFMYHIHNLQHIFDGVRKEIKEVFGE
|
||||
YDKVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIW
|
||||
KDPLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMG
|
||||
AGFQAHLQK
|
||||
|
||||
>seq0043
|
||||
KVKCSFIECCLKESLRLYPSVPHLVRTAVKDMKLPYTLRKGDELFVSTFAMGRMPWIWKD
|
||||
PLEFKPERFAPDPSVYPAFNIAPRICLGRHVALLEGKIAIIKLFTKFKSITAVKSPMGAG
|
||||
FQAHLQK
|
||||
|
||||
>seq0044
|
||||
EYEKVKCRYIECCLKESLRLYPSVPHLVRTAVKDIKLPYTVRPGDEVFVSAYAMGRMPWV
|
||||
WEDPLEFKPERFQPDPSMYPAFNIAPRICLGRHVALLEGKIAIIKLFTKYKSITAVQSPM
|
||||
GAGFQAHLQK
|
||||
|
||||
>seq0045
|
||||
FDLISMFIITDEELRDITFSFIIAGKDTTAQMLSWLMYHLHKLQQVMDNIRAEIRRVFGD
|
||||
YEKVQCQYIECCLKESLRLYPSVPYLVRTPVKDIATHYVIRKGDEVMVAAYSMARMPWLW
|
||||
DDPLAFKPERFMYDPSLYPAFNIAPRICLGRHVALMEGKIAVIKLFSKYKNITAVKSPME
|
||||
TGFKAHLNVR
|
||||
|
||||
>seq0046
|
||||
INFIIAGKDTTAQMLSWFFYHINNLYDIERKMRDEIEEIFGTYEKVKCDYIECCLNETLR
|
||||
LYPSVPHLVRTAVKDIRTPYVIRKGDEIFISAWSMGRAPWIWDEPLQFKPERFMIDPSRF
|
||||
PAFNVAPRICLGKHVALLEGKLALIKIFKKYKHISAVPGPMKVGFKVRMRKE
|
||||
|
||||
>seq0047
|
||||
PFVGHHRIFITNPKIAKQLFDAIKRELLGDGIFATNGQRWREHRAIASHMFTVRSLRDYM
|
||||
FDVFCYTTDQLLDKLEMTVDDVNIYDMYNRLTFEAFTKIAFGVDVGEIRFDRAELRKKEM
|
||||
RSHIDWIEDYIYKVIANRRAYYYDLLSMFLISDKELRDITVNFIIAGKDTTAQMLSWFTY
|
||||
HLHKLIEVENKIRAEITKVFGNYKQVQCTYLECCFLESLRLYPSVPHLARAAVVDIETYY
|
||||
TIRAGDEVLICPLSMSRLEWIWPNAEQFIPERFAFDPWVYPAFNIPPRLCLGKHVALLEG
|
||||
KIALIKLFSRFSSIVRSDAPMPHGYKVHLRKRVEP
|
||||
|
||||
>seq0048
|
||||
IKNIFGKYEDVKCNYIEACLYESLRLYPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSM
|
||||
GRSKYIWEDPMKFNPERFIYEPWVYPAFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQ
|
||||
AFQSAMKNGLKVVLK
|
||||
|
||||
>seq0049
|
||||
IAGRDTTSQMLSWFMFHLTKNDGMDLIEKNIRNEIKNIFGKYEDVKCNYIEACLYESLRL
|
||||
YPSVPNLVRTAIEDIKLPHTIRKGEEIVISTYSMGRSKYIWEDPMKFNPERFIYEPWVYP
|
||||
AFNLKPRLCLGKHVAILEGKIAIIKLFSQFQSIQAFQSAMKNGLKVVLK
|
||||
|
||||
>seq0050
|
||||
YDLLSMFIISDRQLRDITMNFIIAGRDTTSQMLSWFMYHLTNSDMKTIESNIRNEIKTIF
|
||||
GTYDDVKCNYIEACLLESLRLYPSVPNLVRTAIEDIQTPYTIRKNDEIMISTYSIGRSKY
|
||||
IWKDPLTFNPERFLYDPSVYPAFNLKPRLCLGKHVALMEGKIAIIKLFNKFKTIKCVPSA
|
||||
MKNGWKVTLE
|
||||
|
||||
>seq0051
|
||||
YDLLSMFIISDDELRDITMNFIIAGRDTTSHMLSWFLFHLTQNDGMSDIEKKIRNEIDNI
|
||||
FGSYEKVKCEYIEACLYETLRLYPSVPHLLRTAVEDIKTKYTIRKGDDIVISAYAMGRSK
|
||||
YIWDKPLKFDANRFIYDASVYPAFNIQPRLCLGKHVAILEGKIALIKLFSRFKTIKCLPS
|
||||
AMKNGWKLDLK
|
||||
|
||||
>seq0052
|
||||
MLSWFYFHLTQNDGMSEIEKNIRNEIDNIFGSYENVKCEYIEACLYETLRLYPSVPHLLR
|
||||
TAVEDIKTKYTIRKGDDIVISAYAMGRSKYIWDDPLKFDANRFIYDASVYPAFNIQPRLC
|
||||
LGKHVAILEGKIALIKLFTKFKNIKCLPSAMKNGWKLDLK
|
||||
|
||||
>seq0053
|
||||
VECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGDEIIITTFPLGRLPWLWEN
|
||||
ADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVAMFTNFKSFQAVPAAM
|
||||
|
||||
>seq0054
|
||||
IVENIRKEIIQKFGDYDKVECKYIECCLKETLRLYPSVPHFSREMVKDFKVKIYTFYKGD
|
||||
EIIITTFPLGRLPWLWGNADKFIPERFMYDNSQYPAFNIAPRTCLGKNVALLEGKIAVVA
|
||||
MFTNFKSFQAVPAAMDGGFKIHIH
|
||||
|
||||
>seq0055
|
||||
IVENIRKEIIEKFGEYNKVECKYIECCLKETLRLYPSVTHFSREMVKDFKLKIYTFYKGD
|
||||
EIVVTTFAMGRLPWLWKNAEKFVPERFMYDQSKYVAFNISPRTCLGKNVALLEGKIAVIA
|
||||
MFSQFKSFRTVPAAMDGGFNIYVE
|
||||
|
||||
>seq0056
|
||||
IAGRDTTSQMISWFMFHLLNQSNKRNIIIDNIKNEIISVFGEYDKVQCVYLDACLKETLR
|
||||
LYPSVPHFVRQMVTDLTLNIYTFEKGDEIVVFTIALGKLPWLWENADEFIPERFIYDAEI
|
||||
WPAFNIAPRTCLGKNVALMEGKMALIAMFSNFKNFKTVAAPFRNGFKIFLD
|
||||
|
||||
>seq0057
|
||||
YDLLSIFIINDKFLRDVTMNFIIAGRDTTSQMLSWFIFHLLNEDEKRNVIINNIKKEIVD
|
||||
VFGEYDKVKCSYIEACLKETLRLYPSVPHFVREMVSDLTLNIYTFHKGDEVIVCTIALGK
|
||||
LPWLWENANEFIPERFIYDAHIWPAFNIAPRTCLGKNVALLEGKTAIIAMFSNFKKMTTV
|
||||
PAPFRNGFNIYLK
|
||||
|
||||
>seq0058
|
||||
DITMNFIIAGRDTTSQMLSWFMFHLYNEDDKRNVIINNIKNEIISIFGEYNKVKCDYIEA
|
||||
CLKETLRMYPSVPHFVREMVTDMKINIYIFEKGNEIIICTIALGKLPWLWDNANEFIPER
|
||||
FIYDNHIYPAFNILPRTCLGKNVALLEGKIAIISMFSNFNKFKAVP
|
||||
|
||||
>seq0059
|
||||
LLSWFLYLVYENGKKFIEEKILKEIEEKCPNFSELECEYLESALLETLRLYPSVHHLERT
|
||||
AVEDIKLSLEQYIIREGDHIMVEAYALGRATWIWGDDALEFNPLRFYYDPSQYLAFNIAP
|
||||
RICLGKHVALLEAKLVVIKLLRHFTIQPVKSAMKNGYKIILKRR
|
||||
|
||||
>seq0060
|
||||
QNVVFISDPVQTKYIYDRRPMFGHGIFVSDGHEWRKQRKIASRLFTMRNLKHYMFENFET
|
||||
CSKRLVNKLPIDLFDMFNRLTMDGFVASAFGVYSDTIEQAPHDTRFEAFDGGCDRFIARP
|
||||
FLETLKHAKRFCSIRERIESGE
|
||||
|
||||
>seq0061
|
||||
ERIESHDLLSLFMFTEEELQDLCLNFIIAGRDTTAENISWLMYELSKNPHVLQLVIDEIN
|
||||
TLTYDNVELTYLESALLETQRLHPSVPTLNRQAKRDIKLPFTVKKGDIYMVHNYAMGRAP
|
||||
WIWEDPLRFDPTRFSYEPQVFPQFNIAPRMCLGKHVAMME
|
||||
|
||||
>seq0062
|
||||
YNLLSLFLNYTLDELRDICINFIIAGRDTTAETLTWLCVELSSHPDIVDQIRNEINQVTY
|
||||
ESLEMKYTESALLETQRLHPSVPSLIRFAFQDIVLPYTIRKGDAVNVFNYAMGRSPWIWE
|
||||
NPLQFHPPRFQFHPSVYPAFNIGQRLCLGRHVALMHAKVVLYHLFKHFNFKAVPAPLKNG
|
||||
FQVHLQPLHPTQN
|
||||
|
||||
>seq0063
|
||||
DLLTLYAITRSELQDVCVNFIIAGRDTTALNLCWLFILLAQNPHCLQQLKDEIRSISFKT
|
||||
LDMTYTESCILEAQRIYPSVPSLTRVAVTDIPLPYVIHKDEIVVISTFAMNRSPKIWENP
|
||||
LQFDPSRFEHEPHIYPSFNIGQRLCLGRHVALLVAKVVLYHFFQNFDFQIDMAPLTNGLP
|
||||
MRIIPLSSSV
|
||||
|
||||
@ -1,33 +0,0 @@
|
||||
|
||||
|
||||
========================================= NEW GUIDANCE RUN STARTED ===========================================
|
||||
GUIDANCE COMMAND: perl guidance.v2.02/www/Guidance/guidance.pl --bootstraps 10 --seqFile batch2/OG5_126554_0_preguidance.fasta --msaProgram MAFFT --seqType aa --outDir /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance --seqCutoff 0.7 --colCutoff 0.4 --outOrder as_input --MSA_Param \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol
|
||||
Guidance::validate_Seqs(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/,Seqs.Orig.fas,AminoAcids,No): return: OK Seqs.Orig.fas.FIXED 64
|
||||
Guidance::name2codeFastaFrom1(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED, /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes, /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas,0,seqNum);
|
||||
convert_fs_to_upper_case(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas)
|
||||
Align: mafft \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --amino --quiet /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.numberd.fas > /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln
|
||||
Bootstrap_Trees: /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/../../programs/semphy/semphy -a 20 --jtt -H -J -v 8 --BPrepeats=10 -s /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln -o /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.out -T /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.outTree -l /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.log > /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/MSA.MAFFT.semphy.std
|
||||
Guidance::pullOutBPtrees(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/,MSA,10,MAFFT);
|
||||
Guidance::root_BP_trees(/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/,MSA, MAFFT, 10,"",BioPerl);
|
||||
Sample op according to uniform distribution: Guidance::SampleFromUnifomDist(1,3,/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//SampledOPVals.log,10)
|
||||
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_0 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_0/MSA.MAFFT.semphy.tree_0.rooted.GoodBranchLength 19 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.000817428956 >> COS.std
|
||||
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_1 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_1/MSA.MAFFT.semphy.tree_1.rooted.GoodBranchLength 108 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.58462865668747 >> COS.std
|
||||
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_2 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_2/MSA.MAFFT.semphy.tree_2.rooted.GoodBranchLength 82 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 1.49936059497511 >> COS.std
|
||||
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_3 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_3/MSA.MAFFT.semphy.tree_3.rooted.GoodBranchLength 60 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 1.23331485380722 >> COS.std
|
||||
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_4 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_4/MSA.MAFFT.semphy.tree_4.rooted.GoodBranchLength 76 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.15783221114012 >> COS.std
|
||||
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_5 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_5/MSA.MAFFT.semphy.tree_5.rooted.GoodBranchLength 53 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.90590667209469 >> COS.std
|
||||
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_6 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_6/MSA.MAFFT.semphy.tree_6.rooted.GoodBranchLength 57 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.63676633992571 >> COS.std
|
||||
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_7 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_7/MSA.MAFFT.semphy.tree_7.rooted.GoodBranchLength 100 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.80645936921989 >> COS.std
|
||||
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_8 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_8/MSA.MAFFT.semphy.tree_8.rooted.GoodBranchLength 72 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 1.84405518368005 >> COS.std
|
||||
run_HOT_COS_GUIDANCE2: cd /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/; perl /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/exec/HoT_COS_GUIDANCE2.pl MSA_9 MFT aa Seqs.numberd.fas . "" 0 mafft /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/tree_9/MSA.MAFFT.semphy.tree_9.rooted.GoodBranchLength 24 --- \--auto --maxiterate 1000 --thread 6 --bl 62 --anysymbol --op 2.13819830457351 >> COS.std
|
||||
calculating SP scores: /scratch/katzlab/auden/Guidance/General/Seq0.7/guidance.v2.02/www/Guidance/../../programs/msa_set_score/msa_set_score /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.aln /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.Guidance2 -d /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/BP/GUIDANCE2_MSA/ > /Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance//MSA.MAFFT.msa_set_score.std
|
||||
Guidance::codes2name_scoresFile_NEW("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names");
|
||||
Guidance::removeLowSPsites_NoBioPerl ("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Without_low_SP_Col",0.4,"/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.MSA.MAFFT.Removed_Col");
|
||||
REMOVED_SITES:0
|
||||
MSA_LENGTH:351
|
||||
ans=Convert_to_CSV("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv");
|
||||
ANS:OK
|
||||
Guidance::printColoredAlignment_With_CSS("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance_res_pair_res.html","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_res.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv",GUIDANCE2,"/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr");
|
||||
1Guidance::removeLowSPseq ("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_seq.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Without_low_SP_Seq",0.7,"/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Orig.fas.FIXED.Removed_Seq");
|
||||
Guidance::make_Jalview_Color_MSA("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.aln","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_res.scr","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_JalView_Features","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/Seqs.Codes");
|
||||
Guidance::make_Jalview_AnnotationGraph("/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_JalView_Annot","/Users/katzlab/scratch/katzlab/auden/Guidance/General/Seq0.7/GuidanceOutput/OG5_126554_0_preguidance/MSA.MAFFT.Guidance2_res_pair_col.scr.csv",GUIDANCE2." scores");
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,34 +0,0 @@
|
||||
import os, sys
|
||||
from Bio import SeqIO
|
||||
from tqdm import tqdm
|
||||
|
||||
|
||||
prev_recs = [rec.id for rec in SeqIO.parse('AllCuratedNTDSeqs_020722_previous.fasta', 'fasta')]
|
||||
|
||||
recs5 = { rec.id : file[:12] for file in os.listdir('Seq0.5') for rec in SeqIO.parse('Seq0.5/' + file, 'fasta') }
|
||||
recs7 = { rec.id : file[:12] for file in os.listdir('Seq0.5') for rec in SeqIO.parse('Seq0.7/' + file, 'fasta') }
|
||||
|
||||
#print(len(prev_recs))
|
||||
print(recs5)
|
||||
#print(len(recs7))
|
||||
|
||||
n_file = open('NumRemovedSeqs.csv', 'w')
|
||||
seqs5_file = open('AllRemovedSeqs_0.5.csv', 'w')
|
||||
seqs7_file = open('AllRemovedSeqs_0.7.csv', 'w')
|
||||
|
||||
n_by_clade_5 = { }; n_by_clade_7 = { }
|
||||
for rec in prev_recs:
|
||||
if(recs5[rec] not in n_by_clade_5):
|
||||
n_by_clade_5.update({ recs5[rec] : 0 })
|
||||
n_by_clade_7.update({ recs5[rec] : 0 })
|
||||
if(rec not in recs5):
|
||||
seqs5_file.write(rec + '\n')
|
||||
n_by_clade_5[recs5[rec]] += 1
|
||||
if(rec not in recs7):
|
||||
seqs7_file.write(rec + '\n')
|
||||
n_by_clade_7[recs5[rec]] += 1
|
||||
|
||||
|
||||
seqs5_file.close()
|
||||
|
||||
|
||||
@ -1,11 +0,0 @@
|
||||
import os, sys
|
||||
from Bio import SeqIO
|
||||
|
||||
|
||||
nucls = { rec.id : str(rec.seq) for rec in SeqIO.parse('AllCuratedNTDSeqs_020722_previous.fasta', 'fasta') }
|
||||
|
||||
with open('AllCuratedNTDSeqs_022222_Seq0.7.fasta', 'w') as o:
|
||||
for file in os.listdir('SeqFiltered_ToAlign/Preguidance_0.7_Aligned'):
|
||||
if('.fas' in file):
|
||||
for rec in SeqIO.parse('SeqFiltered_ToAlign/Preguidance_0.7_Aligned/' + file, 'fasta'):
|
||||
o.write('>' + rec.id + '\n' + nucls[rec.id] + '\n\n')
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
@ -1,55 +0,0 @@
|
||||
import os, sys, re
|
||||
import ete3
|
||||
from logger import Logger
|
||||
|
||||
|
||||
def get_best_clade(params, tree):
|
||||
|
||||
if params.target_taxa_file != None:
|
||||
try:
|
||||
target_taxa_list = [line.strip() for line in open(PathtoFiles + '/' + target_taxa_list)]
|
||||
except (FileNotFoundError, TypeError):
|
||||
Logger.Error('The --target_taxa_file could not be found or was incorrectly formatted.')
|
||||
|
||||
if params.at_least_file != None:
|
||||
try:
|
||||
at_least_list = [line.strip() for line in open(PathtoFiles + '/' + at_least_file)]
|
||||
except (FileNotFoundError, TypeError):
|
||||
Logger.Error('The --at_least_file could not be found or was incorrectly formatted.')
|
||||
else:
|
||||
at_least_list = []
|
||||
|
||||
|
||||
### FROM HERE BELOW IN THIS FUNCTION NEEDS REPLACING WITH ETE3
|
||||
|
||||
forbidden_nodes = [node for node in nodes_to_exclude]
|
||||
for node in nodes_to_exclude:
|
||||
for num in tree.getNodeNumsAbove(node):
|
||||
forbidden_nodes.append(tree.node(num))
|
||||
|
||||
best_node = None
|
||||
best_size = 0
|
||||
for node in tree.iterNodesNoRoot():
|
||||
if(node not in forbidden_nodes):
|
||||
leaves = tree.getAllLeafNames(node)
|
||||
|
||||
num = 0.0; dem = 0.0;
|
||||
|
||||
non_minor = []
|
||||
for leaf in leaves:
|
||||
if(leaf[:2] != target_minor and leaf[:4] != target_minor):
|
||||
num += 1.0;
|
||||
non_minor.append(leaf[:10])
|
||||
|
||||
if(target_taxa_list == 'na' or target_taxa_list == '' or target_taxa_list == 'NA'):
|
||||
n_targets = len(list(dict.fromkeys([tip[:10] for tip in leaves if(tip[:2] == target_clade or tip[:3] == target_clade or tip[:4] == target_clade or tip[:5] == target_clade or tip[:7] == target_clade or tip[:8] == target_clade)])))
|
||||
else:
|
||||
n_targets = len(list(dict.fromkeys([tip[:10] for tip in leaves if((tip[:2] == target_clade or tip[:3] == target_clade or tip[:4] == target_clade or tip[:5] == target_clade or tip[:7] == target_clade or tip[:8] == target_clade) and (tip[:10] in target_taxa_list or tip[:8] in target_taxa_list))])))
|
||||
|
||||
at_least_taxa = len(list(dict.fromkeys([leaf[:10] for leaf in tree.getAllLeafNames(node) if leaf[:10] in at_least_list])))
|
||||
|
||||
if(num <= cont_num_contams and n_targets > best_size and n_targets >= min_presence and at_least_taxa >= num_at_least):
|
||||
best_node = node
|
||||
best_size = n_targets
|
||||
|
||||
return best_node
|
||||
BIN
PTL2/Scripts-DEV/guidance.v2.02/.DS_Store
vendored
BIN
PTL2/Scripts-DEV/guidance.v2.02/.DS_Store
vendored
Binary file not shown.
@ -1,33 +0,0 @@
|
||||
.PHONY: all libs semphy programs clean install
|
||||
|
||||
all: libs programs
|
||||
|
||||
debug: libs.debug
|
||||
|
||||
%: libs.% programs.%
|
||||
echo $@
|
||||
|
||||
libs: libs.all
|
||||
|
||||
programs: programs.all
|
||||
|
||||
programs.all: libs
|
||||
programs.debug: libs.debug
|
||||
|
||||
semphy: programs.semphy
|
||||
|
||||
install: programs.install
|
||||
|
||||
programs.install programs.all semphy: libs
|
||||
|
||||
clean: libs.clean programs.clean
|
||||
|
||||
libs.%:
|
||||
+cd libs;make $(*)
|
||||
|
||||
programs.%:
|
||||
+cd programs;make $(*)
|
||||
|
||||
tags: libs/*/*.cpp libs/*/*.h programs/*/*.h programs/*/*.cpp
|
||||
etags --members --language=c++ $^
|
||||
|
||||
@ -1,129 +0,0 @@
|
||||
GUIDANCE: GUIDe tree based AligNment ConfidencE
|
||||
|
||||
GUIDANCE is a software package for aligning biological sequences (DNA or
|
||||
amino acids) using either MAFFT, PRANK, or CLUSTALW, and calculating
|
||||
confidence scores for each column, sequence and residue in the alignment.
|
||||
|
||||
URL: http://guidance.tau.ac.il/
|
||||
|
||||
Authors: Osnat Penn, Eyal Privman, Haim Ashkenazy, Itamar Sela, Giddy Landan, Dan Graur, and Tal Pupko.
|
||||
|
||||
When using the GUIDANCE2 algorithm please cite:
|
||||
-----------------------------------------------------------
|
||||
Sela, I., Ashkenazy, H., Katoh, K. and Pupko, T. (2015)
|
||||
GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.
|
||||
Nucleic Acids Research, 2015 Jul 1; 43: W7-W14.; doi: 10.1093/nar/gkq443
|
||||
|
||||
Landan, G., and D. Graur. (2008).
|
||||
Local reliability measures from sets of co-optimal multiple sequence alignments.
|
||||
Pac Symp Biocomput 13:15-24
|
||||
|
||||
When using the GUIDANCE algorithm please cite:
|
||||
-----------------------------------------------------------
|
||||
Penn, O., Privman, E., Landan, G., Graur, D. and Pupko, T. (2010).
|
||||
An alignment confidence score capturing robustness to guide-tree uncertainty.
|
||||
Molecular Biology and Evolution, 2010 Aug;27(8):1759-67; doi:10.1093/molbev/msq066
|
||||
|
||||
When using the HoT algorithm please cite:
|
||||
-----------------------------------------------------------
|
||||
Landan, G., and D. Graur. (2008).
|
||||
Local reliability measures from sets of co-optimal multiple sequence alignments.
|
||||
Pac Symp Biocomput 13:15-24
|
||||
|
||||
Installation
|
||||
============
|
||||
|
||||
1. Unpack the archive by typing:
|
||||
% tar -xzf guidance.v2.01.tgz
|
||||
|
||||
2. Compile the package by typing:
|
||||
% cd guidance.v2.01
|
||||
% make
|
||||
(Running `make' takes a while)
|
||||
|
||||
3. Check if you have the desired alignment program installed:
|
||||
|
||||
MAFFT: Type "mafft" and check that you have version 6.712 or newer.
|
||||
* Else download and install MAFFT from: http://mafft.cbrc.jp/alignment/software/
|
||||
|
||||
PRANK: Type "prank" and check that you have it insalled
|
||||
* Else download and install PRANK from: http://www.ebi.ac.uk/goldman-srv/prank/prank/
|
||||
|
||||
CLUSTALW: Type "clustalw" and check that you have it insalled
|
||||
* Else download and install CLUSTALW from: http://www.ebi.ac.uk/Tools/clustalw2/index.html
|
||||
|
||||
MUSCLE: Type "muscle" and check that you have it insalled
|
||||
* Else download and install MUSCLE from: http://www.drive5.com/muscle/index.htm
|
||||
|
||||
PAGAN: Type "pagan" and check that you have it installed
|
||||
* Else download and install PAGAN from: http://code.google.com/p/pagan-msa/
|
||||
* In case PAGAN is used not for user provided alignment (using --msaFile), mafft is also required to be installed.
|
||||
|
||||
|
||||
4. GUIDANCE also uses Perl, BioPerl and Ruby:
|
||||
* Type "perl -v" and check that you Perl installed.
|
||||
Else download and install it from: http://www.perl.org/
|
||||
* Type "perl -e 'use Bio::SeqIO'" to check that you have BioPerl.
|
||||
Else download and install it from: http://www.bioperl.org/
|
||||
* Type "ruby -version" to check that you have ruby.
|
||||
Else download and install it from: http://www.ruby-lang.org/en/
|
||||
|
||||
Usage
|
||||
=====
|
||||
|
||||
Run the Perl script: guidance.v2.01/www/Guidance/guidance.pl
|
||||
(Note that you cannot move this script out of its directory, because it uses relative paths to other files in other directories. Sorry)
|
||||
GUIDANCE uses flags in the command line arguments: (for help, type: "perl guidance")
|
||||
|
||||
USAGE:perl guidance.pl --seqFile SEQFILE --msaProgram [MAFFT|PRANK|CLUSTALW|MUSCLE] --seqType [aa|nuc|codon] --outDir FULL_PATH_OUTDIR
|
||||
|
||||
Required parameters:
|
||||
--seqFile Input sequence file in FASTA format
|
||||
--seqType Sequence type may be either of: nuc (nucleotides), aa (amino acids),
|
||||
or codon (nucleotides that will be treated as whole codons)
|
||||
--msaProgram The alignment program - may be either MAFFT, PRANK, CLUSTALW or MUSCLE
|
||||
--outDir The output directory were all output files will be created [please provide full and not relative path]
|
||||
(will be created automatically)
|
||||
|
||||
Optional parameters:
|
||||
--program The confidence measure may be GUIDANCE2, GUIDANCE or HoT. default=GUIDANCE2
|
||||
--bootstraps Number of bootstrap iterations. default=100
|
||||
--genCode Genetic code for use in codon sequence. default=1
|
||||
1> Nuclear Standard
|
||||
15> Nuclear Blepharisma
|
||||
6> Nuclear Ciliate
|
||||
10> Nuclear Euplotid
|
||||
2> Mitochondria Vertebrate
|
||||
5> Mitochondria Invertebrate
|
||||
3> Mitochondria Yeast
|
||||
13> Mitochondria Ascidian
|
||||
9> Mitochondria Echinoderm
|
||||
14> Mitochondria Flatworm
|
||||
4> Mitochondria Protozoan
|
||||
--outOrder May be either aligned or as_input. default=aligned
|
||||
--msaFile Input alignment file - not recommended, see documentation online at: guidance.tau.ac.il
|
||||
--seqCutoff Sequence confidence cutoff between 0 to 1. default=0.6
|
||||
--colCutoff Columnd confidence cutoff between 0 to 1. default=0.93
|
||||
--mafft Path to mafft executable. default=mafft
|
||||
--prank Path to prank executable. default=prank
|
||||
--clustalw path to clustalw executable. default=clustalw
|
||||
--muscle path to muscle executable. default=muscle
|
||||
--pagan path to pagan executable. default=pagan
|
||||
--ruby path to ruby executable. default=ruby
|
||||
--dataset Unique name for the Dataset - will be used as prefix to outputs (default=MSA)
|
||||
--MSA_Param: Passing parameters for the alignment program e.g -F to prank. To pass parameter containning '-' in it, add \ before each '-' e.g. \-F for PRANK
|
||||
--proc_num: Number of processors to use (default=1)
|
||||
|
||||
EXAMPLES:
|
||||
|
||||
>perl guidance.pl --seqFile protein.fas --msaProgram MAFFT --seqType aa --outDir /somedir/protein.guidance
|
||||
Will align the amino acid sequences in the fasta file "protein.fas" using MAFFT and output all results to the diretory "/somedir/protein.guidance"
|
||||
|
||||
>perl guidance.pl --seqFile codingSeq.fas --msaProgram PRANK --seqType codon --outDir /somedir/codingSeq.guidance --genCode 2 --bootstraps 30
|
||||
Will align the codon sequences in the fasta file "codingSeq.fas" using PRANK after translation using the vertebrate mitochondrial genetic code and output all results to the diretory "/somedir/codingSeq.guidance". Only 30 bootstrap iterations will be done instead of the default 100 (cut run-time by a factor of 3)
|
||||
|
||||
Copyrights
|
||||
==========
|
||||
|
||||
* To modify the code, or use parts of it for other purposes, permission should be requested. Please contact Tal Pupko: talp@post.tau.ac.il
|
||||
* Please note that the use of the GUIDANCE program is for academic use only
|
||||
@ -1,29 +0,0 @@
|
||||
# $Id: Makefile 942 2006-10-18 12:28:12Z ninio $
|
||||
|
||||
# There might be need for a split (as done in programs/Makefile) becouse of a bug in make 3.80.1 - see
|
||||
# http://www.cygwin.com/ml/cygwin/2004-09/msg01659.html
|
||||
|
||||
LIBS= phylogeny
|
||||
|
||||
# all has to be the FIRST task!
|
||||
TASKS= all clean test depend debug All install doubleRep
|
||||
.PHONY: $(TASKS) $(LIBS)
|
||||
|
||||
define TASKS_template
|
||||
$(1): $$(addsuffix .$(1),$(LIBS))
|
||||
endef
|
||||
|
||||
$(foreach task,$(TASKS),$(eval $(call TASKS_template,$(task))))
|
||||
|
||||
define LIB_template
|
||||
$(1).%:
|
||||
+cd $(1) && make $$(*)
|
||||
endef
|
||||
|
||||
$(foreach lib,$(LIBS),$(eval $(call LIB_template,$(lib))))
|
||||
|
||||
|
||||
|
||||
$(LIBS):
|
||||
+cd $@ && make
|
||||
|
||||
@ -1,82 +0,0 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<projectDescription>
|
||||
<name>phylogeny</name>
|
||||
<comment></comment>
|
||||
<projects>
|
||||
</projects>
|
||||
<buildSpec>
|
||||
<buildCommand>
|
||||
<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
|
||||
<triggers>clean,full,incremental,</triggers>
|
||||
<arguments>
|
||||
<dictionary>
|
||||
<key>?name?</key>
|
||||
<value></value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.append_environment</key>
|
||||
<value>true</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.autoBuildTarget</key>
|
||||
<value>all</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.buildArguments</key>
|
||||
<value></value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.buildCommand</key>
|
||||
<value>make</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.buildLocation</key>
|
||||
<value>${workspace_loc:/phylogeny/Debug}</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
|
||||
<value>clean</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.contents</key>
|
||||
<value>org.eclipse.cdt.make.core.activeConfigSettings</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.enableAutoBuild</key>
|
||||
<value>false</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.enableCleanBuild</key>
|
||||
<value>true</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.enableFullBuild</key>
|
||||
<value>true</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.fullBuildTarget</key>
|
||||
<value>all</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.stopOnError</key>
|
||||
<value>true</value>
|
||||
</dictionary>
|
||||
<dictionary>
|
||||
<key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key>
|
||||
<value>true</value>
|
||||
</dictionary>
|
||||
</arguments>
|
||||
</buildCommand>
|
||||
<buildCommand>
|
||||
<name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
|
||||
<arguments>
|
||||
</arguments>
|
||||
</buildCommand>
|
||||
</buildSpec>
|
||||
<natures>
|
||||
<nature>org.eclipse.cdt.core.ccnature</nature>
|
||||
<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
|
||||
<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
|
||||
<nature>org.eclipse.cdt.core.cnature</nature>
|
||||
</natures>
|
||||
</projectDescription>
|
||||
@ -1,25 +0,0 @@
|
||||
// $Id: AddLog.cpp 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
// version 1.00
|
||||
// last modified 3 Nov 2002
|
||||
|
||||
#include "AddLog.h"
|
||||
#include <cmath>
|
||||
|
||||
const int tAddLog_Precompute::G_LOGADD = 500;
|
||||
const int tAddLog_Precompute::D_LOGADD = 50;
|
||||
|
||||
tAddLog_Precompute AddLogData;
|
||||
|
||||
int tAddLog_Precompute::d_logadd;
|
||||
|
||||
tAddLog_Precompute::tAddLog_Precompute(){
|
||||
d_logadd = int(D_LOGADD*log(10.0)*G_LOGADD);
|
||||
logaddf = new double [d_logadd+1];
|
||||
for (int i=0; i<= d_logadd; i++)
|
||||
logaddf[i] = log(1.0+exp(-static_cast<double>(i)/G_LOGADD));
|
||||
}
|
||||
|
||||
tAddLog_Precompute::~tAddLog_Precompute(){
|
||||
delete [] logaddf;
|
||||
}
|
||||
@ -1,67 +0,0 @@
|
||||
// $Id: AddLog.h 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
// version 1.00
|
||||
// last modified 2 Nov 2002
|
||||
|
||||
#ifndef __AddLog_h
|
||||
#define __AddLog_h
|
||||
|
||||
#include <iostream>
|
||||
using namespace std;
|
||||
|
||||
class tAddLog_Precompute {
|
||||
public:
|
||||
|
||||
tAddLog_Precompute();
|
||||
~tAddLog_Precompute();
|
||||
|
||||
double AddLog( double x, double y );
|
||||
|
||||
private:
|
||||
static const int D_LOGADD; // = 50; // y/x < 1e-D discard
|
||||
static const int G_LOGADD;// = 500; // step function look-up every 1/G
|
||||
static int d_logadd;
|
||||
|
||||
double *logaddf;
|
||||
};
|
||||
|
||||
extern tAddLog_Precompute AddLogData;
|
||||
|
||||
inline
|
||||
double
|
||||
AddLog(double x, double y ){
|
||||
return AddLogData.AddLog(x, y);
|
||||
}
|
||||
|
||||
inline double
|
||||
tAddLog_Precompute::AddLog(double x, double y ){
|
||||
if (x < y) {
|
||||
double dummy = x;
|
||||
x = y;
|
||||
y = dummy;
|
||||
}
|
||||
|
||||
#ifdef notdef
|
||||
return x + log(1 + exp(y-x));
|
||||
#endif
|
||||
|
||||
double z = (x-y)*G_LOGADD;
|
||||
int i = int(z);
|
||||
if( i < d_logadd ) x += ((i+1-z)*logaddf[i] + (z-i)*logaddf[i+1]);
|
||||
return x;
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
/*
|
||||
Folks,
|
||||
|
||||
In many of our program we use the AddLog procedure that compute the sum of
|
||||
two numbers in log form. Gill spent some time investigating faster versions
|
||||
of this procedure, which gave him 3-4 fold speedup on his program. Attached
|
||||
is my re-packaging of his solution. I think it will be useful in some of the
|
||||
code we use.
|
||||
|
||||
-Nir
|
||||
*/
|
||||
Binary file not shown.
@ -1,112 +0,0 @@
|
||||
// $Id: C_evalParamUSSRV.cpp 1915 2007-04-04 15:56:24Z privmane $
|
||||
#include "C_evalParamUSSRV.h"
|
||||
|
||||
// *********************
|
||||
// * USSRV *
|
||||
// *********************
|
||||
|
||||
MDOUBLE C_evalParamUSSRV::operator() (MDOUBLE param) {
|
||||
|
||||
setParam(param);
|
||||
MDOUBLE res = likelihoodComputation2USSRV::getTreeLikelihoodAllPosAlphTheSame(_et,_sc,_baseSc,*_pModel,_weights);
|
||||
print(param,res);
|
||||
return -res;
|
||||
}
|
||||
|
||||
void C_evalAlphaUSSRV::setParam(MDOUBLE alpha)
|
||||
{
|
||||
if (_pModel->noOfCategor() == 1)
|
||||
errorMsg::reportError(" one category when trying to optimize alpha");
|
||||
_pModel->updateAlpha(alpha);
|
||||
}
|
||||
|
||||
void C_evalAlphaUSSRV::print(MDOUBLE alpha,MDOUBLE res) {
|
||||
LOG(5,<<" with Alpha = "<<alpha<<" logL = " <<res<<endl);
|
||||
}
|
||||
|
||||
|
||||
void C_evalNuUSSRV::setParam(MDOUBLE Nu)
|
||||
{
|
||||
_pModel->updateNu(Nu);
|
||||
}
|
||||
|
||||
void C_evalNuUSSRV::print(MDOUBLE nu,MDOUBLE res) {
|
||||
LOG(5,<<" with Nu = "<<nu<<" logL = " <<res<<endl);
|
||||
}
|
||||
|
||||
void C_evalFUSSRV::setParam(MDOUBLE f)
|
||||
{
|
||||
_pModel->updateF(f);
|
||||
}
|
||||
|
||||
void C_evalFUSSRV::print(MDOUBLE f,MDOUBLE res) {
|
||||
LOG(5,<<" with F = "<<f<<" logL = " <<res<<endl);
|
||||
}
|
||||
|
||||
|
||||
// *********************
|
||||
// * SSRV *
|
||||
// *********************
|
||||
|
||||
MDOUBLE C_evalParamSSRV::operator() (MDOUBLE param) {
|
||||
|
||||
setParam(param);
|
||||
MDOUBLE res = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_et,_sc,_ssrvSp,_weights);
|
||||
print(param,res);
|
||||
return -res;
|
||||
}
|
||||
|
||||
void C_evalAlphaSSRV::setParam(MDOUBLE alpha)
|
||||
{
|
||||
if (alpha<0)
|
||||
errorMsg::reportError("ERROR in C_evalAlphaSSRV::setParam, alpha is < 0 ");
|
||||
|
||||
replacementModelSSRV* pMulRM = static_cast<replacementModelSSRV*>(_ssrvSp.getPijAccelerator()->getReplacementModel());
|
||||
gammaDistribution* gammaDist = static_cast<gammaDistribution*>(pMulRM->getDistribution());
|
||||
gammaDist->setAlpha(alpha);
|
||||
pMulRM->updateQ();
|
||||
}
|
||||
|
||||
void C_evalAlphaSSRV::print(MDOUBLE alpha,MDOUBLE res) {
|
||||
LOG(5,<<" with Alpha = "<<alpha<<" logL = " <<res<<endl);
|
||||
}
|
||||
|
||||
|
||||
void C_evalNuSSRV::setParam(MDOUBLE Nu)
|
||||
{
|
||||
if (Nu<0)
|
||||
errorMsg::reportError("C_evalNuSSRV::setParam, nu is < 0 ");
|
||||
|
||||
static_cast<replacementModelSSRV*>(_ssrvSp.getPijAccelerator()->getReplacementModel())->setRateOfRate(Nu);
|
||||
}
|
||||
|
||||
void C_evalNuSSRV::print(MDOUBLE nu,MDOUBLE res) {
|
||||
LOG(5,<<" with Nu = "<<nu<<" logL = " <<res<<endl);
|
||||
}
|
||||
|
||||
void C_evalTrTvSSRV::setParam(MDOUBLE TrTv)
|
||||
{
|
||||
replacementModelSSRV* pMulRM = static_cast<replacementModelSSRV*>(_ssrvSp.getPijAccelerator()->getReplacementModel());
|
||||
static_cast<tamura92*>(pMulRM->getBaseRM())->changeTrTv(TrTv);
|
||||
pMulRM->updateQ();
|
||||
}
|
||||
|
||||
void C_evalTrTvSSRV::print(MDOUBLE TrTv,MDOUBLE res) {
|
||||
LOG(5,<<" with TrTv = "<<TrTv<<" logL = " <<res<<endl);
|
||||
}
|
||||
|
||||
void C_evalThetaSSRV::setParam(MDOUBLE Theta)
|
||||
{
|
||||
replacementModelSSRV* pMulRM = static_cast<replacementModelSSRV*>(_ssrvSp.getPijAccelerator()->getReplacementModel());
|
||||
static_cast<tamura92*>(pMulRM->getBaseRM())->changeTheta(Theta);
|
||||
pMulRM->updateFreq();
|
||||
pMulRM->updateQ();
|
||||
}
|
||||
|
||||
void C_evalThetaSSRV::print(MDOUBLE Theta,MDOUBLE res) {
|
||||
LOG(5,<<" with Theta = "<<Theta<<" logL = " <<res<<endl);
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,177 +0,0 @@
|
||||
// $Id: C_evalParamUSSRV.h 1915 2007-04-04 15:56:24Z privmane $
|
||||
#ifndef ___C_EVAL_PARAM_USSRV
|
||||
#define ___C_EVAL_PARAM_USSRV
|
||||
|
||||
#include "definitions.h"
|
||||
|
||||
#include "likelihoodComputation.h"
|
||||
#include "likelihoodComputation2USSRV.h"
|
||||
#include "sequenceContainer.h"
|
||||
#include "stochasticProcess.h"
|
||||
#include "gammaDistribution.h"
|
||||
#include "tree.h"
|
||||
#include "replacementModelSSRV.h"
|
||||
#include "tamura92.h"
|
||||
#include "stochasticProcessSSRV.h"
|
||||
#include "ussrvModel.h"
|
||||
#include "logFile.h"
|
||||
|
||||
// *********************
|
||||
// * USSRV *
|
||||
// *********************
|
||||
|
||||
class C_evalParamUSSRV {
|
||||
public:
|
||||
C_evalParamUSSRV(const tree& et,
|
||||
const sequenceContainer& sc,
|
||||
const sequenceContainer& baseSc,
|
||||
ussrvModel* pModel,
|
||||
const Vdouble* weights = NULL)
|
||||
: _et(et),_sc(sc),_baseSc(baseSc),_pModel(pModel),_weights(weights){}
|
||||
|
||||
MDOUBLE operator() (MDOUBLE param) ;
|
||||
virtual ~C_evalParamUSSRV(){}
|
||||
|
||||
protected:
|
||||
const tree& _et;
|
||||
const sequenceContainer& _sc;
|
||||
const sequenceContainer& _baseSc;
|
||||
ussrvModel* _pModel;
|
||||
const Vdouble * _weights;
|
||||
|
||||
|
||||
protected:
|
||||
virtual void setParam(MDOUBLE param) = 0;
|
||||
virtual void print(MDOUBLE param,MDOUBLE res) =0;
|
||||
};
|
||||
|
||||
|
||||
class C_evalAlphaUSSRV : public C_evalParamUSSRV {
|
||||
public:
|
||||
C_evalAlphaUSSRV(const tree& et,
|
||||
const sequenceContainer& sc,
|
||||
const sequenceContainer& baseSc,
|
||||
ussrvModel* pModel,
|
||||
const Vdouble *weights = NULL)
|
||||
: C_evalParamUSSRV(et,sc,baseSc,pModel,weights)
|
||||
{}
|
||||
|
||||
protected:
|
||||
virtual void setParam(MDOUBLE alpha);
|
||||
virtual void print(MDOUBLE alpha,MDOUBLE res);
|
||||
};
|
||||
|
||||
|
||||
|
||||
class C_evalNuUSSRV : public C_evalParamUSSRV{
|
||||
public:
|
||||
C_evalNuUSSRV( const tree& et,
|
||||
const sequenceContainer& sc,
|
||||
const sequenceContainer& baseSc,
|
||||
ussrvModel* pModel,
|
||||
const Vdouble * weights = NULL)
|
||||
: C_evalParamUSSRV(et,sc,baseSc,pModel,weights){}
|
||||
|
||||
protected:
|
||||
virtual void setParam(MDOUBLE Nu);
|
||||
virtual void print(MDOUBLE nu,MDOUBLE res);
|
||||
};
|
||||
|
||||
class C_evalFUSSRV : public C_evalParamUSSRV{
|
||||
public:
|
||||
C_evalFUSSRV( const tree& et,
|
||||
const sequenceContainer& sc,
|
||||
const sequenceContainer& baseSc,
|
||||
ussrvModel* pModel,
|
||||
const Vdouble * weights = NULL)
|
||||
: C_evalParamUSSRV(et,sc,baseSc,pModel,weights){}
|
||||
|
||||
protected:
|
||||
virtual void setParam(MDOUBLE F);
|
||||
virtual void print(MDOUBLE f,MDOUBLE res);
|
||||
};
|
||||
|
||||
// *********************
|
||||
// * SSRV *
|
||||
// *********************
|
||||
|
||||
class C_evalParamSSRV {
|
||||
public:
|
||||
C_evalParamSSRV(const tree& et,
|
||||
const sequenceContainer& sc,
|
||||
stochasticProcessSSRV& ssrvSp,
|
||||
const Vdouble* weights = NULL)
|
||||
: _et(et),_sc(sc),_ssrvSp(ssrvSp),_weights(weights){}
|
||||
|
||||
MDOUBLE operator() (MDOUBLE param) ;
|
||||
virtual ~C_evalParamSSRV(){}
|
||||
|
||||
protected:
|
||||
const tree& _et;
|
||||
const sequenceContainer& _sc;
|
||||
stochasticProcessSSRV& _ssrvSp;
|
||||
const Vdouble * _weights;
|
||||
|
||||
|
||||
protected:
|
||||
virtual void setParam(MDOUBLE param) = 0;
|
||||
virtual void print(MDOUBLE param,MDOUBLE res) =0;
|
||||
};
|
||||
|
||||
|
||||
class C_evalAlphaSSRV : public C_evalParamSSRV {
|
||||
public:
|
||||
C_evalAlphaSSRV(const tree& et,
|
||||
const sequenceContainer& sc,
|
||||
stochasticProcessSSRV& ssrvSp,
|
||||
const Vdouble *weights = NULL)
|
||||
: C_evalParamSSRV(et,sc,ssrvSp,weights)
|
||||
{}
|
||||
|
||||
protected:
|
||||
virtual void setParam(MDOUBLE alpha);
|
||||
virtual void print(MDOUBLE alpha,MDOUBLE res);
|
||||
};
|
||||
|
||||
|
||||
|
||||
class C_evalNuSSRV : public C_evalParamSSRV{
|
||||
public:
|
||||
C_evalNuSSRV( const tree& et,
|
||||
const sequenceContainer& sc,
|
||||
stochasticProcessSSRV& ssrvSp,
|
||||
const Vdouble * weights = NULL)
|
||||
: C_evalParamSSRV(et,sc,ssrvSp,weights){}
|
||||
|
||||
protected:
|
||||
virtual void setParam(MDOUBLE Nu);
|
||||
virtual void print(MDOUBLE nu,MDOUBLE res);
|
||||
};
|
||||
|
||||
class C_evalTrTvSSRV : public C_evalParamSSRV{
|
||||
public:
|
||||
C_evalTrTvSSRV(const tree& et,
|
||||
const sequenceContainer& sc,
|
||||
stochasticProcessSSRV& ssrvSp,
|
||||
const Vdouble * weights = NULL)
|
||||
: C_evalParamSSRV(et,sc,ssrvSp,weights){}
|
||||
|
||||
protected:
|
||||
virtual void setParam(MDOUBLE TrTv);
|
||||
virtual void print(MDOUBLE TrTv,MDOUBLE res);
|
||||
};
|
||||
|
||||
class C_evalThetaSSRV : public C_evalParamSSRV{
|
||||
public:
|
||||
C_evalThetaSSRV(const tree& et,
|
||||
const sequenceContainer& sc,
|
||||
stochasticProcessSSRV& ssrvSp,
|
||||
const Vdouble * weights = NULL)
|
||||
: C_evalParamSSRV(et,sc,ssrvSp,weights){}
|
||||
|
||||
protected:
|
||||
virtual void setParam(MDOUBLE Theta);
|
||||
virtual void print(MDOUBLE Theta,MDOUBLE res);
|
||||
};
|
||||
|
||||
#endif
|
||||
Binary file not shown.
@ -1,52 +0,0 @@
|
||||
#include "ConversionUtils.h"
|
||||
#include "someUtil.h"
|
||||
#include "errorMsg.h"
|
||||
|
||||
#include <cmath>
|
||||
|
||||
using namespace std;
|
||||
|
||||
void appendIntToString (string& ioString, const int inValue) {
|
||||
std::ostringstream o;
|
||||
o << ioString<< inValue;
|
||||
ioString = o.str();
|
||||
}
|
||||
|
||||
string appendInt2string(const int x)
|
||||
{
|
||||
string res;
|
||||
appendIntToString(res, x);
|
||||
return res;
|
||||
}
|
||||
|
||||
string appendDouble2string(const double x, const int lenght){
|
||||
|
||||
// first getting the integer part:
|
||||
int theIntegerPart = static_cast<int>(x);
|
||||
double theRemainingPart = fabs(x-theIntegerPart);
|
||||
int integerRepresentingTheRemainingPart = static_cast<int>(theRemainingPart*pow(10.0,lenght));
|
||||
string part1, part2;
|
||||
appendIntToString(part1, theIntegerPart);
|
||||
appendIntToString(part2, integerRepresentingTheRemainingPart);
|
||||
while (part2.length()<lenght){
|
||||
part2.insert(0, "0");
|
||||
}
|
||||
|
||||
string result = part1;
|
||||
result += ".";
|
||||
result += part2;
|
||||
|
||||
// removing 0 from the end
|
||||
int i = result.length()-1;
|
||||
while (result[i]!='.' && i>0 && result[i]=='0'){
|
||||
result.erase(i);
|
||||
i--;
|
||||
}
|
||||
|
||||
// removing "." if this is the last character in the string.
|
||||
if (result[result.length()-1]=='.')
|
||||
result.erase(result.length()-1);
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
@ -1,51 +0,0 @@
|
||||
//utility class that converts between data types
|
||||
#ifndef ___ConversionUtils_h
|
||||
#define ___ConversionUtils_h
|
||||
|
||||
#include <sstream>
|
||||
#include <string>
|
||||
#include "definitions.h"
|
||||
|
||||
using namespace std;
|
||||
|
||||
//a function that turns an integer to string
|
||||
|
||||
void appendIntToString (string& ioString, const int inValue);
|
||||
string appendDouble2string(const double x, int const howManyDigitsAfterTheDot=5);
|
||||
string appendInt2string(const int x);
|
||||
|
||||
|
||||
// Trims spaces at the left side of a string
|
||||
static inline string trim_left(const string& str )
|
||||
{
|
||||
int i=str.find_first_not_of(" \t");
|
||||
if(str.size()==0 || i >= str.size())
|
||||
return str;
|
||||
return str.substr( i ) ;
|
||||
}
|
||||
|
||||
|
||||
////
|
||||
// Trims spaces at the right side of a string
|
||||
static inline string trim_right(const string& str )
|
||||
{
|
||||
int i=str.find_last_not_of(" \t");
|
||||
if(str.size()==0 || i >= str.size())
|
||||
return str;
|
||||
return str.substr(0, i + 1);
|
||||
}
|
||||
|
||||
////
|
||||
// Trims spaces at both sides of a string
|
||||
static inline string trim(const string& str )
|
||||
{
|
||||
return trim_left(trim_right(str));
|
||||
}
|
||||
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Binary file not shown.
@ -1,178 +0,0 @@
|
||||
// $Id: GLaguer.cpp 962 2006-11-07 15:13:34Z privmane $
|
||||
#include "definitions.h"
|
||||
#include "GLaguer.h"
|
||||
|
||||
#include "errorMsg.h"
|
||||
#include "gammaUtilities.h"
|
||||
|
||||
|
||||
|
||||
GLaguer::GLaguer(const int pointsNum, const MDOUBLE alf, Vdouble & points, Vdouble & weights)
|
||||
{
|
||||
gaulag(_points, _weights, alf, pointsNum);
|
||||
|
||||
weights = _weights;
|
||||
points = _points;
|
||||
}
|
||||
|
||||
|
||||
//Input: alf = the alpha parameter of the Laguerre polynomials
|
||||
// pointsNum = the polynom order
|
||||
//Output: the abscissas and weights are stored in the vecotrs x and w, respectively.
|
||||
//Discreption: given alf, the alpha parameter of the Laguerre polynomials, the function returns the abscissas and weights
|
||||
// of the n-point Guass-Laguerre quadrature formula.
|
||||
// The smallest abscissa is stored in x[0], the largest in x[pointsNum - 1].
|
||||
void GLaguer::gaulag(Vdouble &x, Vdouble &w, const MDOUBLE alf, const int pointsNum)
|
||||
{
|
||||
x.resize(pointsNum, 0.0);
|
||||
w.resize(pointsNum, 0.0);
|
||||
const int MAXIT=10000;
|
||||
const MDOUBLE EPS=1.0e-6;
|
||||
int i,its,j;
|
||||
MDOUBLE ai,p1,p2,p3,pp,z=0.0,z1;
|
||||
|
||||
int n= x.size();
|
||||
for (i=0;i<n;i++) {
|
||||
//loops over the desired roots
|
||||
if (i == 0) { //initial guess for the smallest root
|
||||
z=(1.0+alf)*(3.0+0.92*alf)/(1.0+2.4*n+1.8*alf);
|
||||
} else if (i == 1) {//initial guess for the second smallest root
|
||||
z += (15.0+6.25*alf)/(1.0+0.9*alf+2.5*n);
|
||||
} else { //initial guess for the other roots
|
||||
ai=i-1;
|
||||
z += ((1.0+2.55*ai)/(1.9*ai)+1.26*ai*alf/
|
||||
(1.0+3.5*ai))*(z-x[i-2])/(1.0+0.3*alf);
|
||||
}
|
||||
for (its=0;its<MAXIT;its++) { //refinement by Newton's method
|
||||
p1=1.0;
|
||||
p2=0.0;
|
||||
for (j=0;j<n;j++) { //Loop up the recurrence relation to get the Laguerre polynomial evaluated at z.
|
||||
p3=p2;
|
||||
p2=p1;
|
||||
p1=((2*j+1+alf-z)*p2-(j+alf)*p3)/(j+1);
|
||||
}
|
||||
//p1 is now the desired Laguerre polynomial. We next compute pp, its derivative,
|
||||
//by a standard relation involving also p2, the polynomial of one lower order.
|
||||
pp=(n*p1-(n+alf)*p2)/z;
|
||||
z1=z;
|
||||
z=z1-p1/pp; //Newton's formula
|
||||
if (fabs(z-z1) <= EPS)
|
||||
break;
|
||||
}
|
||||
if (its >= MAXIT)
|
||||
errorMsg::reportError("too many iterations in gaulag");
|
||||
x[i]=z;
|
||||
w[i] = -exp(gammln(alf+n)-gammln(MDOUBLE(n)))/(pp*n*p2);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
void GLaguer::GetPhylipLaguer(const int categs, MDOUBLE alpha, Vdouble & points, Vdouble & weights)
|
||||
{
|
||||
/* calculate rates and probabilities to approximate Gamma distribution
|
||||
of rates with "categs" categories and shape parameter "alpha" using
|
||||
rates and weights from Generalized Laguerre quadrature */
|
||||
|
||||
points.resize(categs, 0.0);
|
||||
weights.resize(categs, 0.0);
|
||||
long i;
|
||||
raterootarray lgroot; /* roots of GLaguerre polynomials */
|
||||
double f, x, xi, y;
|
||||
|
||||
alpha = alpha - 1.0;
|
||||
lgroot[1][1] = 1.0+alpha;
|
||||
for (i = 2; i <= categs; i++)
|
||||
{
|
||||
cerr<<lgroot[i][1]<<"\t";
|
||||
lgr(i, alpha, lgroot); /* get roots for L^(a)_n */
|
||||
cerr<<lgroot[i][1]<<endl;
|
||||
}
|
||||
/* here get weights */
|
||||
/* Gamma weights are (1+a)(1+a/2) ... (1+a/n)*x_i/((n+1)^2 [L_{n+1}^a(x_i)]^2) */
|
||||
f = 1;
|
||||
for (i = 1; i <= categs; i++)
|
||||
f *= (1.0+alpha/i);
|
||||
for (i = 1; i <= categs; i++) {
|
||||
xi = lgroot[categs][i];
|
||||
y = glaguerre(categs+1, alpha, xi);
|
||||
x = f*xi/((categs+1)*(categs+1)*y*y);
|
||||
points[i-1] = xi/(1.0+alpha);
|
||||
weights[i-1] = x;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
void GLaguer::lgr(long m, double alpha, raterootarray lgroot)
|
||||
{ /* For use by initgammacat. Get roots of m-th Generalized Laguerre
|
||||
polynomial, given roots of (m-1)-th, these are to be
|
||||
stored in lgroot[m][] */
|
||||
long i;
|
||||
double upper, lower, x, y;
|
||||
bool dwn; /* is function declining in this interval? */
|
||||
|
||||
if (m == 1) {
|
||||
lgroot[1][1] = 1.0+alpha;
|
||||
} else {
|
||||
dwn = true;
|
||||
for (i=1; i<=m; i++) {
|
||||
if (i < m) {
|
||||
if (i == 1)
|
||||
lower = 0.0;
|
||||
else
|
||||
lower = lgroot[m-1][i-1];
|
||||
upper = lgroot[m-1][i];
|
||||
}
|
||||
else { /* i == m, must search above */
|
||||
lower = lgroot[m-1][i-1];
|
||||
x = lgroot[m-1][m-1];
|
||||
do {
|
||||
x = 2.0*x;
|
||||
y = glaguerre(m, alpha,x);
|
||||
} while ((dwn && (y > 0.0)) || ((!dwn) && (y < 0.0)));
|
||||
upper = x;
|
||||
}
|
||||
while (upper-lower > 0.000000001) {
|
||||
x = (upper+lower)/2.0;
|
||||
if (glaguerre(m, alpha, x) > 0.0) {
|
||||
if (dwn)
|
||||
lower = x;
|
||||
else
|
||||
upper = x;
|
||||
}
|
||||
else {
|
||||
if (dwn)
|
||||
upper = x;
|
||||
else
|
||||
lower = x;
|
||||
}
|
||||
}
|
||||
lgroot[m][i] = (lower+upper)/2.0;
|
||||
dwn = !dwn; // switch for next one
|
||||
}
|
||||
}
|
||||
} /* lgr */
|
||||
|
||||
|
||||
double GLaguer::glaguerre(long m, double b, double x)
|
||||
{ /* Generalized Laguerre polynomial computed recursively.
|
||||
For use by initgammacat */
|
||||
long i;
|
||||
double gln, glnm1, glnp1; /* L_n, L_(n-1), L_(n+1) */
|
||||
|
||||
if (m == 0)
|
||||
return 1.0;
|
||||
else {
|
||||
if (m == 1)
|
||||
return 1.0 + b - x;
|
||||
else {
|
||||
gln = 1.0+b-x;
|
||||
glnm1 = 1.0;
|
||||
for (i=2; i <= m; i++) {
|
||||
glnp1 = ((2*(i-1)+b+1.0-x)*gln - (i-1+b)*glnm1)/i;
|
||||
glnm1 = gln;
|
||||
gln = glnp1;
|
||||
}
|
||||
return gln;
|
||||
}
|
||||
}
|
||||
} /* glaguerre */
|
||||
@ -1,30 +0,0 @@
|
||||
// $Id: GLaguer.h 962 2006-11-07 15:13:34Z privmane $
|
||||
#ifndef ___GLAGUER
|
||||
#define ___GLAGUER
|
||||
|
||||
#include "definitions.h"
|
||||
#include <vector>
|
||||
using namespace std;
|
||||
|
||||
typedef double raterootarray[35][35];
|
||||
|
||||
class GLaguer
|
||||
{
|
||||
public:
|
||||
explicit GLaguer(const int pointsNum, const MDOUBLE alpha, Vdouble & points, Vdouble & weights);
|
||||
|
||||
void GetPhylipLaguer(const int pointsNum, MDOUBLE alf, Vdouble & points, Vdouble & weights);
|
||||
|
||||
private:
|
||||
void gaulag(Vdouble &x, Vdouble &w, const MDOUBLE alf, const int pointsNum);
|
||||
|
||||
void lgr(long m, double alpha, raterootarray lgroot);
|
||||
double glaguerre(long m, double b, double x);
|
||||
|
||||
|
||||
private:
|
||||
Vdouble _points;
|
||||
Vdouble _weights;
|
||||
};
|
||||
|
||||
#endif
|
||||
Binary file not shown.
@ -1,156 +0,0 @@
|
||||
#include "GamMixtureOptimizer.h"
|
||||
#include "someUtil.h"
|
||||
#include "optGammaMixtureEM.h"
|
||||
#include "optGammaMixtureLS.h"
|
||||
|
||||
#include <fstream>
|
||||
#include <algorithm>
|
||||
#include <ctime>
|
||||
using namespace std;
|
||||
|
||||
|
||||
|
||||
GamMixtureOptimizer::GamMixtureOptimizer(stochasticProcess* pSp, const sequenceContainer& sc, const tree& inTree, unObservableData* unObservableData_p)
|
||||
{
|
||||
_pSc = ≻
|
||||
_pTree = &inTree;
|
||||
_pSp = pSp;
|
||||
_unObservableData_p = unObservableData_p;
|
||||
_tolOptSpecific = 0.001;
|
||||
|
||||
}
|
||||
|
||||
|
||||
GamMixtureOptimizer::~GamMixtureOptimizer()
|
||||
{
|
||||
}
|
||||
|
||||
|
||||
///////////////////////////////////////////////////////////////////////////////////////////////////////////
|
||||
//findBestParamManyStarts: Finds the best gammaMixture from many starting points.
|
||||
//The function starts form few starting points.
|
||||
//For each point it tries to optimize the likellihood doing only a small number of iterations.
|
||||
//It then picks the best points (highest likelihood) and continue the maximization for these points only.
|
||||
//This can be repeated a number of times, each cycle with a different optimization algorithm.
|
||||
//The best gammaMixture is stored in _sp and the best likelihood is returned.
|
||||
//input Parameters:
|
||||
//pointsNum: a vector with the number of points to peformed the current cycle of optimization.
|
||||
//iterNum: the number of iterations to perform in each cycle.
|
||||
//OptAlgs: the optimization algorithm to be performed in each cycle.
|
||||
//tol = for determining convergence in the maximization process.
|
||||
MDOUBLE GamMixtureOptimizer::findBestParamManyStarts(const Vint pointsNum, const Vint iterNum, const vector<OptimAlg> OptAlgs, const Vdouble tols, const Vdouble * pWeights, ofstream* pOutF/*= NULL*/)
|
||||
{
|
||||
//make sure that the number of points in each cycle is not bigger than the previous cycle.
|
||||
int i;
|
||||
for (i = 0; i < pointsNum.size()-1; ++i)
|
||||
{
|
||||
if (pointsNum[i] < pointsNum[i+1])
|
||||
errorMsg::reportError("input error in GamMixtureOptimizer::findBestParamManyStarts()");
|
||||
}
|
||||
|
||||
//create starting distributions
|
||||
vector<mixtureDistribution*> distVec;
|
||||
const mixtureDistribution * pMixture = getMixtureDist();
|
||||
for (i = 0; i < pointsNum[0]; ++i)
|
||||
{
|
||||
//the first distribution will be the current one
|
||||
if (i == 0)
|
||||
distVec.push_back(new mixtureDistribution(*pMixture));
|
||||
else
|
||||
distVec.push_back(new mixtureDistribution(pMixture->getComponentsNum(), pMixture->categoriesForOneComponent(), LAGUERRE, 15, 15));
|
||||
}
|
||||
|
||||
//make a small number of iterations for all random starts
|
||||
int numOfOptCycles = pointsNum.size();
|
||||
Vdouble likelihoodVec;
|
||||
for (i = 0; i < numOfOptCycles; ++i)
|
||||
{
|
||||
if (i != 0)
|
||||
{
|
||||
vector<mixtureDistribution*> tmpDistVec(0);
|
||||
//sort results and continue optimization only with the best (pointsNum[i]) points
|
||||
Vdouble sortedL = likelihoodVec;
|
||||
sort(sortedL.begin(),sortedL.end());
|
||||
MDOUBLE threshold = sortedL[sortedL.size()- pointsNum[i]];
|
||||
for (int j = 0; j < likelihoodVec.size(); ++j)
|
||||
{
|
||||
if (likelihoodVec[j] >= threshold)
|
||||
tmpDistVec.push_back(distVec[j]);
|
||||
else
|
||||
delete distVec[j];
|
||||
}
|
||||
distVec.clear();
|
||||
distVec = tmpDistVec;
|
||||
}
|
||||
|
||||
likelihoodVec.clear();
|
||||
likelihoodVec.resize(pointsNum[i]);
|
||||
int c;
|
||||
for (c = 0; c < pointsNum[i]; ++c)
|
||||
{
|
||||
cerr <<"optimizing point " <<c<<endl;
|
||||
MDOUBLE ll = optimizeParam(distVec[c], iterNum[i], OptAlgs[i], tols[i], pWeights, pOutF);
|
||||
cerr<<"pointi: "<<c<<" likelihood = "<<ll<<endl;
|
||||
likelihoodVec[c] = ll;
|
||||
}
|
||||
}
|
||||
|
||||
Vdouble sortedL = likelihoodVec;
|
||||
sort(sortedL.begin(),sortedL.end());
|
||||
MDOUBLE bestL = sortedL[likelihoodVec.size() - 1];
|
||||
for (i = 0; i < likelihoodVec.size(); ++i)
|
||||
{
|
||||
if (bestL == likelihoodVec[i])
|
||||
{
|
||||
_pSp->setDistribution(distVec[i]);
|
||||
}
|
||||
delete distVec[i];
|
||||
}
|
||||
distVec.clear();
|
||||
return bestL;
|
||||
}
|
||||
|
||||
MDOUBLE GamMixtureOptimizer::findBestParam(const OptimAlg alg, const int maxIterations, const MDOUBLE tol, const Vdouble * pWeights, ofstream* pOutF)
|
||||
{
|
||||
mixtureDistribution* pInDistribution = static_cast<mixtureDistribution*>(_pSp->distr());
|
||||
return optimizeParam(pInDistribution, maxIterations, alg, tol, pWeights, pOutF);
|
||||
}
|
||||
|
||||
|
||||
MDOUBLE GamMixtureOptimizer::optimizeParam(mixtureDistribution* pInDistribution, const int maxIterations, const OptimAlg alg, const MDOUBLE tol, const Vdouble * pWeights, ofstream* pOutF)
|
||||
{
|
||||
MDOUBLE res = 0.0;
|
||||
switch (alg)
|
||||
{
|
||||
case EM: {
|
||||
optGammaMixtureEM emOpt(*_pSp, *_pSc, *_pTree);
|
||||
res = emOpt.optimizeParam(pInDistribution, maxIterations, tol, _tolOptSpecific, pOutF);
|
||||
break;
|
||||
}
|
||||
case ONE_DIM: {
|
||||
optGammaMixtureLS lsOpt(_pSp, *_pSc, *_pTree,MAXIMUM_ALPHA_PARAM,MAXIMUM_BETA_PARAM,_unObservableData_p);
|
||||
res = lsOpt.optimizeParam(pInDistribution, maxIterations, tol, pWeights, optGammaMixtureLS::ONE_DIM);
|
||||
MDOUBLE resRecompute = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(*_pTree,*_pSc,*_pSp,pWeights,_unObservableData_p);
|
||||
if(!DEQUAL(res,resRecompute)){
|
||||
LOGnOUT(3,<<"--- error: different likelihood after GamMixtureOptimizer::optimizeParam,diff= "<<res-resRecompute <<"\n");
|
||||
}
|
||||
break;
|
||||
}
|
||||
//case TX_CONJUGATE_DERIVATIVES:
|
||||
// {
|
||||
// txGamMixtureOptimizer txOpt(_pSp, *_pSc, *_pTree);
|
||||
// txOpt.setOptimizationParameters(tol, _tolOptSpecific, _tolOptSpecific, _tolOptSpecific);
|
||||
// res = txOpt.optimizeParam(pInDistribution, maxIterations, pWeights, alg, pOutF);
|
||||
// break;
|
||||
// }
|
||||
//case NR_CONJUGATE_DERIVATIVES:
|
||||
// {
|
||||
// optGammaMixtureLS opt(_pSp, *_pSc, *_pTree);
|
||||
// res = opt.optimizeParam(pInDistribution, maxIterations, tol, pWeights, optGammaMixtureLS::CONJUGATE_DERIVATIVES, pOutF);
|
||||
// break;
|
||||
// }
|
||||
default:
|
||||
errorMsg::reportError("unknown optimization algorithm in GamMixtureOptimizer::optimizeParam()");
|
||||
}
|
||||
return res;
|
||||
}
|
||||
@ -1,52 +0,0 @@
|
||||
#ifndef __GAMMIXTURE_OPTIMIZER
|
||||
#define __GAMMIXTURE_OPTIMIZER
|
||||
/************************************************************
|
||||
GamMixtureOptimizer class is used to find the best Gamma mixture parameters.
|
||||
The parameters to otimized are the alpha and beta of each component and the components probabilities.
|
||||
The optimizer can choose between several optimization algorithms (EM, ConjugateDerivatives, etc).
|
||||
The interface to the optimizer is the functions:
|
||||
1. findBestParam() = given a gammaMixture - finds the best parameters.
|
||||
2. findBestParamManyStarts() - finds the best parameters but starts from many initial points.
|
||||
3. SetOptAlg() - choose the optimization algorithm to be used.
|
||||
************************************************************/
|
||||
#include "definitions.h"
|
||||
#include "stochasticProcess.h"
|
||||
#include "sequenceContainer.h"
|
||||
#include "tree.h"
|
||||
#include "mixtureDistribution.h"
|
||||
#include "unObservableData.h"
|
||||
|
||||
|
||||
|
||||
class GamMixtureOptimizer{
|
||||
public:
|
||||
enum OptimAlg {EM, ONE_DIM, TX_CONJUGATE_DERIVATIVES, NR_CONJUGATE_DERIVATIVES};
|
||||
public:
|
||||
|
||||
explicit GamMixtureOptimizer(stochasticProcess* cur_sp, const sequenceContainer& sc, const tree& inTree, unObservableData* unObservableData_p = NULL);
|
||||
virtual ~GamMixtureOptimizer();
|
||||
|
||||
const stochasticProcess* getSp() const {return _pSp;}
|
||||
const mixtureDistribution* getMixtureDist() const {return static_cast<mixtureDistribution*>(_pSp->distr());}
|
||||
|
||||
MDOUBLE findBestParamManyStarts(const Vint pointsNum, const Vint iterNum, const vector<OptimAlg> OptAlgs, const Vdouble tols, const Vdouble * pWeights, ofstream* pOutF = NULL);
|
||||
//return the logLikelihood. the final distribution is stored in the stochasticProcess
|
||||
MDOUBLE findBestParam(const OptimAlg alg, const int maxIterations, const MDOUBLE tol, const Vdouble * pWeights, ofstream* pOutF=NULL);
|
||||
|
||||
void setTolOptSpecific(const MDOUBLE tol) {_tolOptSpecific = tol;}
|
||||
|
||||
private:
|
||||
MDOUBLE optimizeParam(mixtureDistribution* pInDistribution, const int maxIterations, const OptimAlg alg, const MDOUBLE tol, const Vdouble * pWeights, ofstream* pOutF);
|
||||
|
||||
|
||||
private:
|
||||
stochasticProcess* _pSp;
|
||||
const sequenceContainer* _pSc;
|
||||
const tree* _pTree;
|
||||
unObservableData* _unObservableData_p;
|
||||
|
||||
MDOUBLE _tolOptSpecific; //tolerance specific to the optimization algorithm
|
||||
};
|
||||
|
||||
#endif
|
||||
|
||||
Binary file not shown.
@ -1,24 +0,0 @@
|
||||
""
|
||||
"0.16315391 "
|
||||
"0.0026528488 0.15680618 "
|
||||
"0.77200021 0.0026528488 9.3704985 "
|
||||
"0.065662251 0.18661252 0.045663061 0.0026528488 "
|
||||
"0.029241185 1.8153444 0.35657046 0.0026528488 0.0026528488 "
|
||||
"0.7859595 0.039751241 0.042054709 5.6172481 0.0026528488 1.3583647 "
|
||||
"1.1329574 1.9384101 0.17158679 1.5057888 0.47638319 0.032849536 2.0839453 "
|
||||
"0.044971782 4.796584 4.0566567 1.0170492 0.12737547 3.7434084 0.063530422 0.0026528488 "
|
||||
"0.0026528488 0.35934906 0.3610872 0.0093800488 0.0026528488 0.0026528488 0.0032315889 0.0026528488 0.054707578 "
|
||||
"0.11420832 0.37215595 0.0026528488 0.0046480457 0.068855751 0.79296833 0.0026528488 0.0026528488 0.92409864 3.1615537 "
|
||||
"0.0026528488 10.850151 4.1938515 0.0026528488 0.0026528488 3.4738365 2.4484839 0.27680089 0.0026528488 0.17101271 0.04324117 "
|
||||
"0.009902713 1.3338205 0.0026528488 0.0026528488 0.0026528488 0.1611213 0.093268326 0.0026528488 0.0026528488 5.9458299 2.8224242 0.68043448 "
|
||||
"0.0074953058 0.0026528488 0.0026528488 0.0026528488 4.9333171 0.0026528488 0.0026528488 0.15469345 0.077228672 1.803067 4.5230222 0.018180397 0.099760378 "
|
||||
"1.1259592 0.68101281 0.0039239772 0.018180397 0.0026528488 2.3727663 0.0063788279 0.0026528488 1.3015831 0.021784823 1.1022958 0.016652568 0.0026528488 0.0026528488 "
|
||||
"1.3085601 1.8459052 6.9741802 0.28026286 2.4900381 0.061711098 0.0026528488 2.324113 0.20307398 0.64624988 0.49218621 0.26746605 0.0026528488 0.50747511 2.8532025 "
|
||||
"8.4457685 1.5220348 3.6538588 0.14576024 0.39260517 0.12924096 0.15374532 0.19610654 0.37755025 4.5693569 0.023221606 2.4785142 2.6211525 0.0074953058 1.0686577 4.7385556 "
|
||||
"0.0026528488 0.52597396 0.0026528488 0.0026528488 1.3968681 0.014142867 0.0026528488 0.64556544 0.036884095 0.0026528488 0.39731344 0.0026528488 0.047262092 0.44002431 0.023584144 0.013196755 0.0026528488 "
|
||||
"0.0026528488 0.0052623288 0.93601524 0.35795048 4.0213579 0.059971891 0.042054709 0.0026528488 9.9186301 0.078613459 0.059416384 0.0026528488 0.0026528488 8.13894 0.016149535 0.34382193 0.056055755 0.67924601 "
|
||||
"4.0399067 0.043106352 0.014142867 0.55599996 0.22285362 0.011097026 0.54567507 0.50571521 0.0026528488 9.4117238 0.74829436 0.14104083 3.6361006 0.38374731 0.0026528488 0.039751241 0.37629386 0.0026528488 0.021784823 "
|
||||
|
||||
|
||||
|
||||
"0.060490222 0.066039665 0.044127815 0.042109048 0.020075899 0.053606488 0.071567447 0.072308239 0.022293943 0.069730629 0.098851122 0.056968211 0.019768318 0.028809447 0.046025282 0.05060433 0.053636813 0.033011601 0.028350243 0.061625237 "
|
||||
@ -1,23 +0,0 @@
|
||||
""
|
||||
"0.021810606 "
|
||||
"0.18082842 0.046923924 "
|
||||
"1.2987859 0.019752881 8.6119047 "
|
||||
"0.049094712 0.83857481 0.017714543 0.0014641764 "
|
||||
"0.0014641764 3.1258994 0.10016958 0.0014641764 0.0014641764 "
|
||||
"1.6291158 0.0073686726 0.059013922 3.5501299 0.0014641764 0.93899388 "
|
||||
"0.54716271 3.9350911 0.017714543 3.0445791 0.014343013 0.017714543 4.3281346 "
|
||||
"0.0014641764 2.0041793 2.5180202 0.67873067 0.0014641764 5.4310694 0.0014641764 0.0014641764 "
|
||||
"0.0014641764 0.39260132 0.28903662 0.042497426 0.0014641764 0.010022346 0.011435569 0.0014641764 0.0014641764 "
|
||||
"0.046923924 0.17182315 0.0014641764 0.0014641764 0.0014641764 0.8464345 0.038021439 0.014343013 0.51650871 2.6655214 "
|
||||
"0.17358807 11.681111 3.1232346 0.26188639 0.0014641764 3.8275035 7.0170946 0.081825497 0.065612672 0.23938727 0.0014641764 "
|
||||
"0.0014641764 0.96240899 0.059013922 0.0014641764 0.0014641764 0.0014641764 0.0014641764 0.014343013 0.0014641764 5.0679244 3.3336075 1.1993479 "
|
||||
"0.17509295 0.0014641764 0.0014641764 0.0014641764 0.1062872 0.0014641764 0.0014641764 0.0014641764 0.0014641764 0.43423957 2.1926949 0.0014641764 0.0014641764 "
|
||||
"0.29570799 0.11851717 0.10098366 0.0014641764 0.0014641764 0.89168927 0.0014641764 0.0014641764 4.0834122 0.0014641764 2.8788489 0.032776467 0.0014641764 0.010022346 "
|
||||
"2.5166849 2.4452448 4.2665807 0.12529865 0.32854654 0.046923924 0.0014641764 1.838906 0.21235155 0.21672475 1.7991682 0.0014641764 0.11495981 1.2531563 4.1726098 "
|
||||
"7.0696878 0.27181058 1.3300754 0.18460189 0.0014641764 0.059472209 0.13433613 0.014343013 0.28099302 2.7419485 0.0014641764 1.185403 2.170826 0.033533153 1.2700295 1.856807 "
|
||||
"0.0014641764 1.7469498 0.0014641764 0.0014641764 1.6102836 0.012981329 0.0014641764 0.82749392 0.0014641764 0.0014641764 0.40127511 0.0014641764 0.0014641764 0.0014641764 0.0014641764 0.32257563 0.0014641764 "
|
||||
"0.0014641764 0.0014641764 1.4831375 0.66811539 2.4446914 0.0014641764 0.0014641764 0.0014641764 13.906425 0.033533153 0.0014641764 0.0014641764 0.16960961 1.2086132 0.0014641764 0.27325689 0.14366733 0.0014641764 "
|
||||
"7.2650675 0.081825497 0.021810606 0.85445233 0.0014641764 0.0014641764 0.64409704 0.81883185 0.24231504 7.2690793 0.86487141 0.037501949 4.3246792 0.66766443 0.0014641764 0.25261054 0.0014641764 0.0014641764 0.39673909 "
|
||||
|
||||
|
||||
"0.0377494 0.057321 0.0891129 0.0342034 0.0240105 0.0437824 0.0618606 0.0838496 0.0156076 0.0983641 0.0577867 0.0641682 0.0158419 0.0422741 0.0458601 0.0550846 0.0813774 0.019597 0.0205847 0.0515639 "
|
||||
@ -1,67 +0,0 @@
|
||||
#include "KH_calculation.h"
|
||||
|
||||
namespace KH_calculation {
|
||||
|
||||
double get_phi (double z)
|
||||
{
|
||||
// constants
|
||||
double a1 = 0.254829592;
|
||||
double a2 = -0.284496736;
|
||||
double a3 = 1.421413741;
|
||||
double a4 = -1.453152027;
|
||||
double a5 = 1.061405429;
|
||||
double p = 0.3275911;
|
||||
|
||||
// Save the sign of z
|
||||
int sign = 1;
|
||||
if (z < 0)
|
||||
{
|
||||
sign = -1;
|
||||
}
|
||||
z = fabs(z)/sqrt(2.0);
|
||||
|
||||
// A&S formula 7.1.26
|
||||
double t = 1.0/(1.0 + p*z);
|
||||
double y = 1.0 - (((((a5*t + a4)*t) + a3)*t + a2)*t + a1)*t*exp(-z*z);
|
||||
|
||||
return 0.5*(1.0 + sign*y);
|
||||
}
|
||||
|
||||
|
||||
double calc_p_value_kh (const Vdouble & LogLikePerPositionA, const Vdouble & LogLikePerPositionB)
|
||||
{
|
||||
//calc esteemated variance of delta of KH (Assessing the Uncertainty in Phylogenetic Inference, Nielsen, pg 484)
|
||||
//delta(X) = LL(A) - LL(B)
|
||||
//H0: E(delta(X)) <= 0 ---> tree B is either better or equal to tree A
|
||||
//H1: E(delta(X)) > 0 ---> tree A is better than tree B
|
||||
int num_pos = LogLikePerPositionA.size();
|
||||
double varDeltaX = 0;
|
||||
double sum_diffs = 0;
|
||||
double avg_diff = 0;
|
||||
for (int i=0; i < num_pos; ++i)
|
||||
{
|
||||
sum_diffs += (LogLikePerPositionA[i] - LogLikePerPositionB[i]);
|
||||
}
|
||||
avg_diff = sum_diffs / num_pos;
|
||||
|
||||
double sum_squares = 0;
|
||||
double sqr_diff = 0;
|
||||
for (int i=0; i < num_pos; ++i)
|
||||
{
|
||||
sqr_diff = pow (LogLikePerPositionA[i] - LogLikePerPositionB[i] - avg_diff, 2);
|
||||
sum_squares += sqr_diff;
|
||||
}
|
||||
varDeltaX = (num_pos / (num_pos - 1)) * sum_squares;
|
||||
//end calc esteemated variance of delta of KH (Assessing the Uncertainty in Phylogenetic Inference, Nielsen, pg 484)
|
||||
|
||||
//obtain the standard test statistic, z:
|
||||
double stdDeltaX = sqrt (varDeltaX);
|
||||
double z = sum_diffs / stdDeltaX; //let's hope stdDeltaX is not a zero
|
||||
|
||||
double phi_of_z = get_phi (z);
|
||||
double p_value = 1 - phi_of_z; //one-sided test to see if A is better than B
|
||||
|
||||
return p_value;
|
||||
}
|
||||
|
||||
};
|
||||
@ -1,16 +0,0 @@
|
||||
// Kishino-Hasegawa Test 2013 02 27 Eli Levy Karin
|
||||
|
||||
#ifndef ___KH_CALCULATION
|
||||
#define ___KH_CALCULATION
|
||||
|
||||
#include "math.h"
|
||||
#include <cmath>
|
||||
#include "definitions.h"
|
||||
|
||||
namespace KH_calculation {
|
||||
double calc_p_value_kh (const Vdouble & LogLikePerPositionA, const Vdouble & LogLikePerPositionB);
|
||||
|
||||
double get_phi (double z);
|
||||
};
|
||||
|
||||
#endif
|
||||
Binary file not shown.
@ -1,23 +0,0 @@
|
||||
" 0.425093 "
|
||||
" 0.276818 0.751878 "
|
||||
" 0.395144 0.123954 5.076149 "
|
||||
" 2.489084 0.534551 0.528768 0.062556 "
|
||||
" 0.969894 2.807908 1.695752 0.523386 0.084808 "
|
||||
" 1.038545 0.363970 0.541712 5.243870 0.003499 4.128591 "
|
||||
" 2.066040 0.390192 1.437645 0.844926 0.569265 0.267959 0.348847 "
|
||||
" 0.358858 2.426601 4.509238 0.927114 0.640543 4.813505 0.423881 0.311484 "
|
||||
" 0.149830 0.126991 0.191503 0.010690 0.320627 0.072854 0.044265 0.008705 0.108882 "
|
||||
" 0.395337 0.301848 0.068427 0.015076 0.594007 0.582457 0.069673 0.044261 0.366317 4.145067 "
|
||||
" 0.536518 6.326067 2.145078 0.282959 0.013266 3.234294 1.807177 0.296636 0.697264 0.159069 0.137500 "
|
||||
" 1.124035 0.484133 0.371004 0.025548 0.893680 1.672569 0.173735 0.139538 0.442472 4.273607 6.312358 0.656604 "
|
||||
" 0.253701 0.052722 0.089525 0.017416 1.105251 0.035855 0.018811 0.089586 0.682139 1.112727 2.592692 0.023918 1.798853 "
|
||||
" 1.177651 0.332533 0.161787 0.394456 0.075382 0.624294 0.419409 0.196961 0.508851 0.078281 0.249060 0.390322 0.099849 0.094464 "
|
||||
" 4.727182 0.858151 4.008358 1.240275 2.784478 1.223828 0.611973 1.739990 0.990012 0.064105 0.182287 0.748683 0.346960 0.361819 1.338132 "
|
||||
" 2.139501 0.578987 2.000679 0.425860 1.143480 1.080136 0.604545 0.129836 0.584262 1.033739 0.302936 1.136863 2.020366 0.165001 0.571468 6.472279 "
|
||||
" 0.180717 0.593607 0.045376 0.029890 0.670128 0.236199 0.077852 0.268491 0.597054 0.111660 0.619632 0.049906 0.696175 2.457121 0.095131 0.248862 0.140825 "
|
||||
" 0.218959 0.314440 0.612025 0.135107 1.165532 0.257336 0.120037 0.054679 5.306834 0.232523 0.299648 0.131932 0.481306 7.803902 0.089613 0.400547 0.245841 3.151815 "
|
||||
" 2.547870 0.170887 0.083688 0.037967 1.959291 0.210332 0.245034 0.076701 0.119013 10.649107 1.702745 0.185202 1.898718 0.654683 0.296501 0.098369 2.188158 0.189510 0.249313 "
|
||||
|
||||
" 0.079066 0.055941 0.041977 0.053052 0.012937 0.040767 0.071586 0.057337 0.022355 0.062157 "
|
||||
" 0.099081 0.064600 0.022951 0.042302 0.044040 0.061197 0.053287 0.012066 0.034155 0.069147 "
|
||||
" Si Quang Le and Olivier Gascuel (LG) matrix "
|
||||
@ -1,245 +0,0 @@
|
||||
#! /usr/local/bin/gmake
|
||||
# $Id: Makefile 15479 2016-10-10 16:25:21Z elilevy $
|
||||
# makfile for yaep5
|
||||
|
||||
|
||||
|
||||
# use LOGREP=t or DOUBLEREP=t to activate logRep or doubleRep respectively (or setenv DOUBLEREP in the shell)
|
||||
#DOUBLEREP=t
|
||||
#LOGREP=t
|
||||
|
||||
|
||||
Libsources= AddLog.cpp NNiProp.cpp NNiSep.cpp Nni.cpp aaJC.cpp \
|
||||
allTrees.cpp allTreesSeparateModel.cpp alphabet.cpp amino.cpp \
|
||||
bestAlpha.cpp bestAlphaManyTrees.cpp bestHKYparam.cpp bootstrap.cpp \
|
||||
bblEM.cpp bblEMfixRoot.cpp bblEMProprtional.cpp bblEMProportionalEB.cpp bblLSProportionalEB.cpp bblEMSeperate.cpp \
|
||||
chebyshevAccelerator.cpp clustalFormat.cpp codon.cpp codonJC.cpp \
|
||||
computeCounts.cpp computeDownAlg.cpp computeMarginalAlg.cpp \
|
||||
computePijComponent.cpp computeUpAlg.cpp computeUpAlgFactors.cpp \
|
||||
computeSubstitutionCounts.cpp \
|
||||
computePosteriorExpectationOfSubstitutions.cpp \
|
||||
computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp \
|
||||
ConversionUtils.cpp countTableComponent.cpp datMatrixHolder.cpp distanceTable.cpp \
|
||||
distribution.cpp errorMsg.cpp evaluateCharacterFreq.cpp \
|
||||
fastStartTree.cpp fastaFormat.cpp findRateOfGene.cpp \
|
||||
fromCountTableComponentToDistance.cpp fromCountTableComponentToDistancefixRoot.cpp \
|
||||
fromCountTableComponentToDistanceProp.cpp fromCountTableComponentToDistancePropEB.cpp fromQtoPt.cpp \
|
||||
generalGammaDistributionFixedCategories.cpp gammaDistribution.cpp gammaUtilities.cpp \
|
||||
generalGammaDistribution.cpp getRandomWeights.cpp goldmanYangModel.cpp \
|
||||
granthamChemicalDistances.cpp hky.cpp simulateWithDependence.cpp KH_calculation.cpp likeDist.cpp likeDistfixRoot.cpp \
|
||||
likeDistProp.cpp likeDistPropEB.cpp likelihoodComputation.cpp \
|
||||
likelihoodComputationFactors.cpp logFile.cpp maseFormat.cpp \
|
||||
molphyFormat.cpp nexusFormat.cpp nj.cpp njConstrain.cpp \
|
||||
nucJC.cpp nucleotide.cpp numRec.cpp Parameters.cpp phylipFormat.cpp \
|
||||
pijAccelerator.cpp readDatMatrix.cpp readTree.cpp recognizeFormat.cpp \
|
||||
replacementModel.cpp searchStatus.cpp seqContainerTreeMap.cpp \
|
||||
sequence.cpp sequenceContainer.cpp simulateTree.cpp \
|
||||
siteSpecificRate.cpp someUtil.cpp split.cpp splitMap.cpp \
|
||||
splitTreeUtil.cpp stochasticProcess.cpp suffStatComponent.cpp \
|
||||
talRandom.cpp tree.cpp treeIt.cpp treeUtil.cpp uniDistribution.cpp \
|
||||
uniformDistribution.cpp cmdline2EvolObjs.cpp \
|
||||
generalGammaDistributionLaguerre.cpp gammaDistributionLaguerre.cpp GLaguer.cpp \
|
||||
givenRatesMLDistance.cpp distanceBasedSeqs2Tree.cpp \
|
||||
posteriorDistance.cpp pairwiseGammaDistance.cpp doubleRep.cpp \
|
||||
logRep.cpp indel.cpp indelModel.cpp mulAlphabet.cpp \
|
||||
replacementModelSSRV.cpp stochasticProcessSSRV.cpp bestAlphaAndNu.cpp \
|
||||
C_evalParamUSSRV.cpp matrixUtils.cpp betaOmegaDistribution.cpp \
|
||||
betaUtilities.cpp betaDistribution.cpp geneticCodeHolder.cpp \
|
||||
samplingSequences.cpp bblEM2USSRV.cpp bestParamUSSRV.cpp \
|
||||
likeDist2USSRV.cpp ussrvModel.cpp likelihoodComputation2USSRV.cpp \
|
||||
fromCountTableComponentToDistance2USSRV.cpp normalDist.cpp \
|
||||
tamura92.cpp bestTamura92param.cpp phylipSequentialFormat.cpp \
|
||||
simulateCodonsJumps.cpp \
|
||||
simulateJumpsAbstract.cpp \
|
||||
ssrvDistanceSeqs2Tree.cpp multipleStochasticProcess.cpp distributionPlusInvariant.cpp\
|
||||
extremeValDistribution.cpp \
|
||||
gammaDistributionFixedCategories.cpp generalGammaDistributionPlusInvariant.cpp gammaDistributionPlusInvariant.cpp \
|
||||
distributionPlusCategory.cpp simulateJumps.cpp computeJumps.cpp seqeuncesFilter.cpp \
|
||||
optGammaMixtureLS.cpp mixtureDistribution.cpp suffStatGammaMixture.cpp GamMixtureOptimizer.cpp optGammaMixtureEM.cpp gainLossAlphabet.cpp \
|
||||
wYangModel.cpp codonUtils.cpp likelihoodComputation2Codon.cpp likeDist2Codon.cpp unObservableData.cpp likelihoodComputationGL.cpp \
|
||||
threeStateModel.cpp threeStateAlphabet.cpp oneTwoMoreModel.cpp betaDistributionFixedCategories.cpp betaDistributionFixedCategoriesWithOmegaUniform.cpp \
|
||||
bblEM2codon.cpp bestAlphaAndK.cpp fromCountTableComponentToDistance2Codon.cpp\
|
||||
gtrModel.cpp bestGtrModelParams.cpp simulateRateShiftJumps.cpp integerAlphabet.cpp
|
||||
|
||||
# do not use: fromInstructionFile.cpp, simulateSequnce.cpp split.save.cpp
|
||||
|
||||
|
||||
# LibCsources= cmdline.c
|
||||
# LibCsources += getopt.c getopt1.c
|
||||
|
||||
EXEC =
|
||||
#TEST_EXEC_SUB = split_test splitMap_test bootstrap_test
|
||||
TEST_EXEC = $(addprefix tests/,$(TEST_EXEC_SUB))
|
||||
LIB = libEvolTree.a
|
||||
DEBUGLIB = $(LIB:.a=Debug.a)
|
||||
DOUBLEREPLIB = $(LIB:.a=DoubleRep.a)
|
||||
|
||||
|
||||
#CC=g++
|
||||
CXX=g++
|
||||
CC=$(CXX)
|
||||
|
||||
#requres 2.13, but may work with 2.11
|
||||
GENGETOPT = gengetopt
|
||||
# osX/tiger
|
||||
#GENGETOPT = /opt/local/bin/gengetopt
|
||||
|
||||
.SECONDARY: semphy_cmdline.c semphy_cmdline.h
|
||||
|
||||
#LDFLAGS=
|
||||
|
||||
CPPFLAGS= -O3 -Wall -Wno-sign-compare -I. -DLOG
|
||||
CPPFLAGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -DVERBOS
|
||||
#CPPFLAGSDOU= $(CPPFLAGS)
|
||||
#-pg
|
||||
|
||||
|
||||
#CPPFLAGS+= -I/usr/include/g++-v3
|
||||
#CPPFLAGS+= -DLOG -DLOGCLS -DMEMCHK
|
||||
|
||||
# sources
|
||||
sources= $(Libsources) $(LibCsources) $(addsuffix .cpp,$(EXEC) $(TEST_EXEC))
|
||||
|
||||
.PHONY: tests lib test debug %.debug
|
||||
.PHONY: dat DOUBLEREP doubleRep
|
||||
|
||||
all: lib $(EXEC)
|
||||
|
||||
test: all tests
|
||||
+cd tests; make -k test
|
||||
|
||||
ifdef DOUBLEREP
|
||||
CPPFLAGS+= -DLOGREP
|
||||
CPPFLAGSDEBUG += -DLOGREP
|
||||
LDFLAGSDEBUG += -DLOGREP
|
||||
endif
|
||||
|
||||
#ifdef DOUBLEREP
|
||||
#CPPFLAGS+= -DDOUBLEREP
|
||||
#CPPFLAGSDEBUG += -DDOUBLEREP
|
||||
#LDFLAGSDEBUG += -DDOUBLEREP
|
||||
#endif
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG
|
||||
debug: $(DEBUGLIB)
|
||||
pl:
|
||||
@echo "lib ="$(LIB)
|
||||
@echo "debug="$(DEBUGLIB)
|
||||
#debug: all
|
||||
# cp libEvolTree.a libEvolTreeDebug.a
|
||||
|
||||
# <<<<<<< Makefile
|
||||
# %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-25
|
||||
# % debug: LIB = libEvolTreeDebug.a
|
||||
# %.debug: %
|
||||
# @echo "made \""$(*)"\" in debug mode"
|
||||
|
||||
# =======
|
||||
#>>>>>>> 2.34
|
||||
|
||||
lib: $(LIB)
|
||||
|
||||
$(LIB): $(Libsources:.cpp=.o) $(LibCsources:.c=.o)
|
||||
ar rv $@ $?
|
||||
ranlib $@
|
||||
|
||||
tags: *.cpp *.h
|
||||
etags --members --language=c++ $^
|
||||
|
||||
$(EXEC) $(TEST_EXEC): $(LIB)
|
||||
tests: $(TEST_EXEC)
|
||||
|
||||
-include make.dep
|
||||
|
||||
install:
|
||||
cd ../fast; make -f Makefile.lib install_do
|
||||
|
||||
|
||||
clean:
|
||||
-rm -f $(LIB) $(DEBUGLIB) $(DOUBLEREPLIB) $(EXEC) $(TEST_EXEC) *.o
|
||||
|
||||
|
||||
ifneq ($(wildcard make.dep), make.dep)
|
||||
make.dep: depend
|
||||
endif
|
||||
|
||||
depend makedep: _make.dep
|
||||
@mv -f _make.dep make.dep
|
||||
|
||||
_make.dep: $(sources)
|
||||
@echo making depend
|
||||
# $(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@ ; [ -s $@ ] || rm -f $@'
|
||||
@$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed "s/\(^[^.]*\)\.o/\1.o \1.debug.o/g" > $@'
|
||||
_fast:
|
||||
cd ../fast;make -f Makefile.lib -k all
|
||||
|
||||
fast.% _fast.%:
|
||||
cd ../fast;make -f Makefile.lib -k $(*)
|
||||
|
||||
|
||||
simulateSequnce: simulateSequnce_cmdline.o
|
||||
|
||||
|
||||
evolObjsTest.ggo: evolObjs.header evolObjs.args
|
||||
cat $^ > $@
|
||||
|
||||
|
||||
# commandline (gengetopts)
|
||||
%_cmdline.h %_cmdline.c: %.ggo
|
||||
$(GENGETOPT) -i$< -F$(*)_cmdline
|
||||
|
||||
%.dat.q: %.dat
|
||||
awk 'BEGIN{RS="[\n\r]+";};{print "\" "$$0" \"\r"}' $< > $@
|
||||
# cat $@
|
||||
|
||||
DAT = cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q
|
||||
|
||||
dat: $(DAT)
|
||||
|
||||
cleandat:
|
||||
rm $(DAT)
|
||||
|
||||
datMatrixHolder.o: $(DAT)
|
||||
|
||||
.PRECIOUS: $(DAT)
|
||||
|
||||
debug: LIB = $(DEBUGLIB)
|
||||
|
||||
%.debug: CPPFLAGS = $(CPPFLAGSDEBUG)
|
||||
%.debug: %
|
||||
@echo "made \""$(*)"\" in debug mode"
|
||||
|
||||
|
||||
%.debug.o: %.c
|
||||
$(CC) -c $(CPPFLAGSDEBUG) $(CFLAGS) $< -o $@
|
||||
|
||||
%.debug.o: %.cpp
|
||||
$(CXX) -c $(CPPFLAGSDEBUG) $(CXXFLAGS) $< -o $@
|
||||
|
||||
$(DEBUGLIB): $(Libsources:.cpp=.debug.o) $(LibCsources:.c=.debug.o)
|
||||
ar rv $@ $?
|
||||
ranlib $@
|
||||
|
||||
doubleRep: LOGREP=t
|
||||
doubleRep: CPPFLAGS+= -DLOGREP
|
||||
#doubleRep: DOUBLEREP=t
|
||||
#doubleRep: CPPFLAGS+= -DDOUBLEREP
|
||||
doubleRep: $(DOUBLEREPLIB)
|
||||
|
||||
%.doubleRep.o: %.c
|
||||
$(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@
|
||||
|
||||
%.doubleRep.o: %.cpp
|
||||
$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@
|
||||
|
||||
$(DOUBLEREPLIB): $(Libsources:.cpp=.doubleRep.o) $(LibCsources:.c=.doubleRep.o)
|
||||
ar rv $@ $?
|
||||
ranlib $@
|
||||
|
||||
# DO NOT DELETE
|
||||
@ -1,139 +0,0 @@
|
||||
// $Id: NNiProp.cpp 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#include "definitions.h"
|
||||
#include "treeIt.h"
|
||||
#include "treeUtil.h"
|
||||
#include "NNiProp.h"
|
||||
#include "bblEM.h"
|
||||
#include "bblEMProportional.h"
|
||||
#include "logFile.h"
|
||||
#include <algorithm>
|
||||
#include <iostream>
|
||||
#include <iomanip>
|
||||
using namespace std;
|
||||
|
||||
NNiProp::NNiProp(vector<sequenceContainer>& sc,
|
||||
vector<stochasticProcess>& sp,
|
||||
const vector<Vdouble *> * weights,
|
||||
vector<char>* nodeNotToSwap):_nodeNotToSwap(nodeNotToSwap),
|
||||
_sc(sc),_sp(sp),_weights(weights) {
|
||||
_bestScore = VERYSMALL;
|
||||
_treeEvaluated =-1;
|
||||
_out = NULL;
|
||||
|
||||
}
|
||||
|
||||
void NNiProp::setOfstream(ostream* out) {
|
||||
_out = out;
|
||||
}
|
||||
|
||||
tree NNiProp::NNIstep(tree et) {
|
||||
et.create_names_to_internal_nodes();
|
||||
_bestScore = evalTree(et);
|
||||
_bestTree = et;
|
||||
treeIterTopDown tIt(et);
|
||||
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
|
||||
if (mynode->isLeaf() || mynode->isRoot()) continue; // swaping only internal nodes
|
||||
|
||||
if (_nodeNotToSwap) {
|
||||
if ((*_nodeNotToSwap)[mynode->id()]) {
|
||||
continue;
|
||||
}
|
||||
}
|
||||
tree newT1 = NNIswap1(et,mynode);
|
||||
tree newT2 = NNIswap2(et,mynode);
|
||||
MDOUBLE treeScore1 = evalTree(newT1);
|
||||
if (treeScore1 > _bestScore) {
|
||||
_bestTree = newT1;
|
||||
_bestScore = treeScore1;
|
||||
LOG(5,<<"new Best Tree: "<<_bestScore<<endl);
|
||||
if (_out) (*_out)<<"new Best Tree: "<<_bestScore<<endl;
|
||||
_bestTree.output(*_out);
|
||||
|
||||
}
|
||||
MDOUBLE treeScore2 = evalTree(newT2);
|
||||
if (treeScore2 > _bestScore) {
|
||||
_bestTree = newT2;
|
||||
_bestScore = treeScore2;
|
||||
LOG(5,<<"new Best Tree: "<<_bestScore<<endl);
|
||||
if (_out) (*_out)<<"new Best Tree: "<<_bestScore<<endl;
|
||||
_bestTree.output(*_out);
|
||||
}
|
||||
}
|
||||
return _bestTree;
|
||||
}
|
||||
|
||||
tree NNiProp::NNIswap1(tree et,tree::nodeP mynode) {
|
||||
tree::nodeP mynodeInNewTree = et.findNodeByName(mynode->name());
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"b4 swap1"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
|
||||
tree::nodeP fatherNode = mynodeInNewTree->father();
|
||||
tree::nodeP nodeToSwap1 = mynodeInNewTree->father()->getSon(0);
|
||||
// it might be me
|
||||
if (nodeToSwap1 == mynodeInNewTree) nodeToSwap1 = mynodeInNewTree->father()->getSon(1);
|
||||
tree::nodeP nodeToSwap2 = mynodeInNewTree->getSon(0);
|
||||
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap1);
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap2);
|
||||
nodeToSwap2->setFather(fatherNode);
|
||||
fatherNode->setSon(nodeToSwap2);
|
||||
nodeToSwap1->setFather(mynodeInNewTree);
|
||||
mynodeInNewTree->setSon(nodeToSwap1);
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"after swap1"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
|
||||
return et;
|
||||
}
|
||||
|
||||
tree NNiProp::NNIswap2(tree et,tree::nodeP mynode) {
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"b4 swap2"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
tree::nodeP mynodeInNewTree = et.findNodeByName(mynode->name());
|
||||
|
||||
|
||||
tree::nodeP fatherNode = mynodeInNewTree->father();
|
||||
tree::nodeP nodeToSwap1 = mynodeInNewTree->father()->getSon(0);
|
||||
// it might be me
|
||||
if (nodeToSwap1 == mynodeInNewTree) nodeToSwap1 = mynodeInNewTree->father()->getSon(1);
|
||||
tree::nodeP nodeToSwap2 = mynodeInNewTree->getSon(1);
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap1);
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap2);
|
||||
nodeToSwap2->setFather(fatherNode);
|
||||
fatherNode->setSon(nodeToSwap2);
|
||||
nodeToSwap1->setFather(mynodeInNewTree);
|
||||
mynodeInNewTree->setSon(nodeToSwap1);
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"after swap2"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
return et;
|
||||
|
||||
}
|
||||
|
||||
MDOUBLE NNiProp::evalTree(tree& et) {
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"b4 bbl in alltrees"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
bblEMProportional bblEMprop1(et,_sc,_sp,_weights);
|
||||
MDOUBLE res = bblEMprop1.getTreeLikelihood();
|
||||
// MDOUBLE res = 12;
|
||||
_treeEvaluated++;
|
||||
// cerr.precision(5);
|
||||
_out->precision(5);
|
||||
|
||||
if (_treeEvaluated) LOG(5,<<"tree: "<<_treeEvaluated<< "score = "<<res<<endl);
|
||||
if ((_out)&&(_treeEvaluated)) (*_out)<<"tree: "<<_treeEvaluated<< "score = "<<res<<endl;
|
||||
return res;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,39 +0,0 @@
|
||||
// $Id: NNiProp.h 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#ifndef ___NNI_PROP
|
||||
#define ___NNI_PROP
|
||||
#include "definitions.h"
|
||||
#include "tree.h"
|
||||
#include "sequenceContainer.h"
|
||||
#include "definitions.h"
|
||||
#include "stochasticProcess.h"
|
||||
#include <vector>
|
||||
using namespace std;
|
||||
|
||||
class NNiProp {
|
||||
public:
|
||||
explicit NNiProp(vector<sequenceContainer>& sc,
|
||||
vector<stochasticProcess>& sp,
|
||||
const vector<Vdouble *> * weights,
|
||||
vector<char>* nodeNotToSwap);
|
||||
|
||||
tree NNIstep(tree et);
|
||||
MDOUBLE bestScore(){ return _bestScore;}
|
||||
void setOfstream(ostream* out);
|
||||
private:
|
||||
ostream* _out;
|
||||
vector<char> * _nodeNotToSwap;
|
||||
private:
|
||||
tree _bestTree;
|
||||
MDOUBLE _bestScore;
|
||||
vector<sequenceContainer>& _sc;
|
||||
vector<stochasticProcess>& _sp;
|
||||
const vector<Vdouble *> * _weights;
|
||||
|
||||
MDOUBLE evalTree(tree& et);
|
||||
tree NNIswap1(tree et,tree::nodeP mynode);
|
||||
tree NNIswap2(tree et,tree::nodeP mynode);
|
||||
int _treeEvaluated;
|
||||
|
||||
};
|
||||
#endif
|
||||
Binary file not shown.
@ -1,174 +0,0 @@
|
||||
// $Id: NNiSep.cpp 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#include "definitions.h"
|
||||
#include "treeIt.h"
|
||||
#include "treeUtil.h"
|
||||
#include "NNiSep.h"
|
||||
#include "bblEM.h"
|
||||
#include "logFile.h"
|
||||
#include "bblEMSeperate.h"
|
||||
|
||||
#include <algorithm>
|
||||
#include <iostream>
|
||||
#include <iomanip>
|
||||
|
||||
using namespace std;
|
||||
|
||||
NNiSep::NNiSep(vector<sequenceContainer>& sc,
|
||||
vector<stochasticProcess>& sp,
|
||||
const vector<Vdouble *> * weights,
|
||||
vector<char>* nodeNotToSwap): _nodeNotToSwap(nodeNotToSwap),
|
||||
_sc(sc),_sp(sp),_weights(weights) {
|
||||
_bestTrees.resize(sc.size());
|
||||
_bestScore=VERYSMALL;
|
||||
_treeEvaluated =-1;
|
||||
|
||||
}
|
||||
|
||||
void NNiSep::setOfstream(ostream* out) {
|
||||
_out = out;
|
||||
}
|
||||
|
||||
|
||||
vector<tree> NNiSep::NNIstep(vector<tree> et) {
|
||||
const int nGene = et.size();
|
||||
int z;
|
||||
for (z=0; z < nGene; ++z) {
|
||||
et[z].create_names_to_internal_nodes();
|
||||
}
|
||||
_bestTrees = et;
|
||||
_bestScore = evalTrees(_bestTrees);
|
||||
|
||||
treeIterTopDown tIt(et[0]);
|
||||
|
||||
vector<tree::nodeP> mynode(nGene);
|
||||
mynode[0] = tIt.first();
|
||||
for (z=1; z < nGene; ++z ) {
|
||||
mynode[z] = et[z].findNodeByName(mynode[0]->name());
|
||||
}
|
||||
|
||||
while (mynode[0] != tIt.end()) {
|
||||
bool haveToBeChecked = true;
|
||||
if ((mynode[0]->isLeaf() || mynode[0]->isRoot())) haveToBeChecked = false;
|
||||
if (_nodeNotToSwap) {
|
||||
if ((*_nodeNotToSwap)[mynode[0]->id()]) {
|
||||
haveToBeChecked = false;
|
||||
}
|
||||
}
|
||||
|
||||
if (haveToBeChecked) { // swaping only internal nodes that are not "fixed"
|
||||
for (z=1; z < nGene; ++z ) {
|
||||
mynode[z] = et[z].findNodeByName(mynode[0]->name());
|
||||
}
|
||||
|
||||
vector<tree> newT1;
|
||||
vector<tree> newT2;
|
||||
|
||||
for (z=0; z < nGene; ++z ) {
|
||||
newT1.push_back(NNIswap1(et[z],mynode[z]));
|
||||
newT2.push_back(NNIswap2(et[z],mynode[z]));
|
||||
}
|
||||
MDOUBLE treeScore1 = evalTrees(newT1);
|
||||
if (treeScore1 > _bestScore) {
|
||||
_bestTrees = newT1;
|
||||
_bestScore = treeScore1;
|
||||
LOG(5,<<"new Best Trees: "<<_bestScore<<endl);
|
||||
if (_out) (*_out)<<"new Best Tree: "<<_bestScore<<endl;
|
||||
if (_out) (*_out)<<"tree topology (of gene 1 in case of many genes): "<<endl;
|
||||
_bestTrees[0].output(*_out);
|
||||
}
|
||||
MDOUBLE treeScore2 = evalTrees(newT2);
|
||||
if (treeScore2 > _bestScore) {
|
||||
_bestTrees = newT2;
|
||||
_bestScore = treeScore2;
|
||||
LOG(5,<<"new Best Trees: "<<_bestScore<<endl);
|
||||
if (_out) (*_out)<<"new Best Tree: "<<_bestScore<<endl;
|
||||
if (_out) (*_out)<<"tree topology (of gene 1 in case of many genes): "<<endl;
|
||||
_bestTrees[0].output(*_out);
|
||||
}
|
||||
}
|
||||
//nextloop:
|
||||
mynode[0] = tIt.next();
|
||||
}
|
||||
return _bestTrees;
|
||||
}
|
||||
|
||||
tree NNiSep::NNIswap1(tree et,tree::nodeP mynode) {
|
||||
tree::nodeP mynodeInNewTree = et.findNodeByName(mynode->name());
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"b4 swap1"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
|
||||
tree::nodeP fatherNode = mynodeInNewTree->father();
|
||||
tree::nodeP nodeToSwap1 = mynodeInNewTree->father()->getSon(0);
|
||||
// it might be me
|
||||
if (nodeToSwap1 == mynodeInNewTree) nodeToSwap1 = mynodeInNewTree->father()->getSon(1);
|
||||
tree::nodeP nodeToSwap2 = mynodeInNewTree->getSon(0);
|
||||
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap1);
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap2);
|
||||
nodeToSwap2->setFather(fatherNode);
|
||||
fatherNode->setSon(nodeToSwap2);
|
||||
nodeToSwap1->setFather(mynodeInNewTree);
|
||||
mynodeInNewTree->setSon(nodeToSwap1);
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"after swap1"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
|
||||
return et;
|
||||
}
|
||||
|
||||
tree NNiSep::NNIswap2(tree et,tree::nodeP mynode) {
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"b4 swap2"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
tree::nodeP mynodeInNewTree = et.findNodeByName(mynode->name());
|
||||
|
||||
|
||||
tree::nodeP fatherNode = mynodeInNewTree->father();
|
||||
tree::nodeP nodeToSwap1 = mynodeInNewTree->father()->getSon(0);
|
||||
// it might be me
|
||||
if (nodeToSwap1 == mynodeInNewTree) nodeToSwap1 = mynodeInNewTree->father()->getSon(1);
|
||||
tree::nodeP nodeToSwap2 = mynodeInNewTree->getSon(1);
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap1);
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap2);
|
||||
nodeToSwap2->setFather(fatherNode);
|
||||
fatherNode->setSon(nodeToSwap2);
|
||||
nodeToSwap1->setFather(mynodeInNewTree);
|
||||
mynodeInNewTree->setSon(nodeToSwap1);
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"after swap2"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
return et;
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
MDOUBLE NNiSep::evalTrees(vector<tree>& et) {
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"b4 bbl in alltrees"<<endl);
|
||||
for (vector<tree>::const_iterator i=et.begin();i!=et.end();++i)
|
||||
LOGDO(5,i->output(myLog::LogFile()));
|
||||
#endif
|
||||
bblEMSeperate bblemsep1(et,_sc,_sp,_weights);
|
||||
MDOUBLE res = bblemsep1.getTreeLikelihood();
|
||||
_treeEvaluated++;
|
||||
LOG(5,.precision(5));
|
||||
_out->precision(5);
|
||||
|
||||
|
||||
if (_treeEvaluated) LOG(5,<<"tree: "<<_treeEvaluated<< "score = "<<res<<endl);
|
||||
if ((_out)&&(_treeEvaluated)) (*_out)<<"tree: "<<_treeEvaluated<< "score = "<<res<<endl;
|
||||
return res;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,40 +0,0 @@
|
||||
// $Id: NNiSep.h 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#ifndef ___NNI_SEP
|
||||
#define ___NNI_SEP
|
||||
|
||||
#include "definitions.h"
|
||||
#include "tree.h"
|
||||
#include "sequenceContainer.h"
|
||||
#include "definitions.h"
|
||||
#include "stochasticProcess.h"
|
||||
#include <vector>
|
||||
using namespace std;
|
||||
|
||||
class NNiSep {
|
||||
public:
|
||||
explicit NNiSep(vector<sequenceContainer>& sc,
|
||||
vector<stochasticProcess>& sp,
|
||||
const vector<Vdouble *> * weights,
|
||||
vector<char>* nodeNotToSwap);
|
||||
|
||||
vector<tree> NNIstep(vector<tree> et);
|
||||
MDOUBLE bestScore(){ return _bestScore;}
|
||||
void setOfstream(ostream* out);
|
||||
|
||||
private:
|
||||
vector<char>* _nodeNotToSwap;
|
||||
vector<tree> _bestTrees;
|
||||
MDOUBLE _bestScore;
|
||||
vector<sequenceContainer>& _sc;
|
||||
vector<stochasticProcess>& _sp;
|
||||
const vector<Vdouble *> * _weights;
|
||||
|
||||
MDOUBLE evalTrees(vector<tree>& et);
|
||||
tree NNIswap1(tree et,tree::nodeP mynode);
|
||||
tree NNIswap2(tree et,tree::nodeP mynode);
|
||||
int _treeEvaluated;
|
||||
ostream* _out;
|
||||
|
||||
};
|
||||
#endif
|
||||
Binary file not shown.
@ -1,119 +0,0 @@
|
||||
// $Id: Nni.cpp 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
// version 1.00
|
||||
// last modified 3 Nov 2002
|
||||
#include "definitions.h"
|
||||
#include "treeUtil.h"
|
||||
#include "treeIt.h"
|
||||
#include "Nni.h"
|
||||
#include "bblEM.h"
|
||||
#include "logFile.h"
|
||||
#include <algorithm>
|
||||
#include <iostream>
|
||||
using namespace std;
|
||||
|
||||
NNI::NNI(const sequenceContainer& sc,
|
||||
const stochasticProcess& sp,
|
||||
const Vdouble * weights): _sc(sc),_sp(sp),_weights(weights) {
|
||||
_bestScore = VERYSMALL;
|
||||
}
|
||||
|
||||
|
||||
tree NNI::NNIstep(tree et) {
|
||||
et.create_names_to_internal_nodes();
|
||||
treeIterTopDown tIt(et);
|
||||
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
|
||||
if (mynode->isLeaf() || mynode->isRoot()) continue; // swaping only internal nodes
|
||||
tree newT1 = NNIswap1(et,mynode);
|
||||
tree newT2 = NNIswap2(et,mynode);
|
||||
MDOUBLE treeScore1 = evalTree(newT1,_sc);
|
||||
MDOUBLE treeScore2 = evalTree(newT2,_sc);
|
||||
if (treeScore1 > _bestScore) {
|
||||
_bestTree = newT1;
|
||||
_bestScore = treeScore1;
|
||||
LOG(5,<<"new Best Tree: "<<_bestScore<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
}
|
||||
if (treeScore2 > _bestScore) {
|
||||
_bestTree = newT2;
|
||||
_bestScore = treeScore2;
|
||||
LOG(5,<<"new Best Tree: "<<_bestScore<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
}
|
||||
}
|
||||
return _bestTree;
|
||||
}
|
||||
|
||||
tree NNI::NNIswap1(tree et,tree::nodeP mynode) {
|
||||
tree::nodeP mynodeInNewTree = et.findNodeByName(mynode->name());
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"b4 swap1"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
|
||||
tree::nodeP fatherNode = mynodeInNewTree->father();
|
||||
tree::nodeP nodeToSwap1 = mynodeInNewTree->father()->getSon(0);
|
||||
// it might be me
|
||||
if (nodeToSwap1 == mynodeInNewTree)
|
||||
nodeToSwap1 = mynodeInNewTree->father()->getSon(1);
|
||||
tree::nodeP nodeToSwap2 = mynodeInNewTree->getSon(0);
|
||||
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap1);
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap2);
|
||||
nodeToSwap2->setFather(fatherNode);
|
||||
fatherNode->setSon(nodeToSwap2);
|
||||
nodeToSwap1->setFather(mynodeInNewTree);
|
||||
mynodeInNewTree->setSon(nodeToSwap1);
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"after swap1"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
|
||||
return et;
|
||||
}
|
||||
|
||||
tree NNI::NNIswap2(tree et,tree::nodeP mynode) {
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"b4 swap2"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
tree::nodeP mynodeInNewTree = et.findNodeByName(mynode->name());
|
||||
|
||||
|
||||
tree::nodeP fatherNode = mynodeInNewTree->father();
|
||||
tree::nodeP nodeToSwap1 = mynodeInNewTree->father()->getSon(0);
|
||||
// it might be me
|
||||
if (nodeToSwap1 == mynodeInNewTree)
|
||||
nodeToSwap1 = mynodeInNewTree->father()->getSon(1);
|
||||
tree::nodeP nodeToSwap2 = mynodeInNewTree->getSon(1);
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap1);
|
||||
et.removeNodeFromSonListOfItsFather(nodeToSwap2);
|
||||
nodeToSwap2->setFather(fatherNode);
|
||||
fatherNode->setSon(nodeToSwap2);
|
||||
nodeToSwap1->setFather(mynodeInNewTree);
|
||||
mynodeInNewTree->setSon(nodeToSwap1);
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"after swap2"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif //VERBOS
|
||||
return et;
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
MDOUBLE NNI::evalTree(tree& et,const sequenceContainer& sc) {
|
||||
#ifdef VERBOS
|
||||
LOG(5,<<"b4 bbl in alltrees"<<endl);
|
||||
LOGDO(5,et.output(myLog::LogFile()));
|
||||
#endif
|
||||
bblEM bblEM1(et,sc,_sp,_weights);
|
||||
MDOUBLE res = bblEM1.getTreeLikelihood();
|
||||
return res;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,32 +0,0 @@
|
||||
// $Id: Nni.h 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#ifndef ___NNI
|
||||
#define ___NNI
|
||||
|
||||
#include "definitions.h"
|
||||
#include "tree.h"
|
||||
#include "sequenceContainer.h"
|
||||
#include "stochasticProcess.h"
|
||||
#include <vector>
|
||||
using namespace std;
|
||||
|
||||
class NNI {
|
||||
public:
|
||||
explicit NNI(const sequenceContainer& sc,
|
||||
const stochasticProcess& sp,
|
||||
const Vdouble * weights);
|
||||
|
||||
tree NNIstep(tree et);
|
||||
MDOUBLE bestScore(){ return _bestScore;}
|
||||
|
||||
private:
|
||||
tree _bestTree;
|
||||
MDOUBLE _bestScore;
|
||||
const sequenceContainer& _sc;
|
||||
const stochasticProcess& _sp;
|
||||
const Vdouble * _weights;
|
||||
MDOUBLE evalTree(tree& et,const sequenceContainer& sd);
|
||||
tree NNIswap1(tree et,tree::nodeP mynode);
|
||||
tree NNIswap2(tree et,tree::nodeP mynode);
|
||||
};
|
||||
#endif
|
||||
Binary file not shown.
@ -1,360 +0,0 @@
|
||||
#include <iostream>
|
||||
#include <sstream>
|
||||
#include <vector>
|
||||
#include "Parameters.h"
|
||||
#include "ConversionUtils.h"
|
||||
#include <stdio.h>
|
||||
#include <cstdlib>
|
||||
using namespace std;
|
||||
|
||||
typedef Parameters::ParamType ParamType;
|
||||
|
||||
class Parameter
|
||||
{
|
||||
public:
|
||||
|
||||
Parameter();
|
||||
Parameter(const string& name, const int val);
|
||||
Parameter(const string& name, const float val);
|
||||
Parameter(const string& name, const string& val);
|
||||
Parameter(const Parameter& param);
|
||||
|
||||
void dump(FILE* outputFile) const;
|
||||
|
||||
~Parameter() {}
|
||||
const string& paramLabel() const;
|
||||
ParamType paramType() const;
|
||||
|
||||
int intValue() const;
|
||||
float floatValue() const;
|
||||
const string& stringValue() const;
|
||||
|
||||
Parameter& operator=(const Parameter& param);
|
||||
|
||||
friend bool operator<(const Parameter& p, const Parameter& q);
|
||||
friend ostream& operator<<(ostream& out, const Parameter& p);
|
||||
|
||||
private:
|
||||
string paramName;
|
||||
ParamType type;
|
||||
union {
|
||||
int i;
|
||||
float f;
|
||||
};
|
||||
string s;
|
||||
};
|
||||
|
||||
typedef vector<Parameter> ParamList;
|
||||
|
||||
static ParamList paramList;
|
||||
|
||||
Parameter::Parameter() : paramName(), type(Parameters::Undef)
|
||||
{}
|
||||
|
||||
Parameter::Parameter(const string& name, const int val)
|
||||
{
|
||||
paramName = name;
|
||||
i = val;
|
||||
type = Parameters::Int;
|
||||
}
|
||||
|
||||
Parameter::Parameter(const string& name, const float val)
|
||||
{
|
||||
paramName = name;
|
||||
f = val;
|
||||
type = Parameters::Float;
|
||||
}
|
||||
|
||||
Parameter::Parameter(const string& name, const string& val)
|
||||
{
|
||||
paramName = name;
|
||||
s = val;
|
||||
type = Parameters::Str;
|
||||
}
|
||||
Parameter::Parameter(const Parameter& param)
|
||||
{
|
||||
paramName = param.paramName;
|
||||
type = param.type;
|
||||
if (type == Parameters::Int)
|
||||
i = param.i;
|
||||
else
|
||||
f = param.f;
|
||||
s = param.s;
|
||||
}
|
||||
|
||||
|
||||
const string& Parameter::paramLabel() const
|
||||
{
|
||||
return paramName;
|
||||
}
|
||||
|
||||
ParamType Parameter::paramType() const
|
||||
{
|
||||
return type;
|
||||
}
|
||||
|
||||
int Parameter::intValue() const
|
||||
{
|
||||
return i;
|
||||
}
|
||||
|
||||
float Parameter::floatValue() const
|
||||
{
|
||||
return f;
|
||||
}
|
||||
|
||||
const string& Parameter::stringValue() const
|
||||
{
|
||||
return s;
|
||||
}
|
||||
|
||||
Parameter& Parameter::operator=(const Parameter& param)
|
||||
{
|
||||
paramName = param.paramName;
|
||||
type = param.type;
|
||||
if (type == Parameters::Int)
|
||||
i = param.i;
|
||||
else
|
||||
f = param.f;
|
||||
s = param.s;
|
||||
return *this;
|
||||
}
|
||||
|
||||
bool operator<(const Parameter& p, const Parameter& q)
|
||||
{
|
||||
return (p.paramName < q.paramName);
|
||||
}
|
||||
|
||||
ostream& operator<<(ostream& out, const Parameter& p) {
|
||||
switch(p.type) {
|
||||
case Parameters::Int:
|
||||
return out << p.paramName << '\t' << "(Int)" << '\t' << p.i;
|
||||
case Parameters::Float:
|
||||
return out << p.paramName << '\t' << "(Float)" << '\t' << p.f;
|
||||
case Parameters::Str:
|
||||
return out << p.paramName << '\t' << "(Str)" << '\t' << p.s;
|
||||
case Parameters::Undef:
|
||||
break;
|
||||
}
|
||||
return out << '\n';
|
||||
}
|
||||
|
||||
|
||||
void Parameter::dump(FILE* outputFile) const {
|
||||
switch(type) {
|
||||
case Parameters::Int:
|
||||
fprintf(outputFile, "%s = %d", paramName.c_str(), i);
|
||||
case Parameters::Float:
|
||||
fprintf(outputFile, "%s = %f", paramName.c_str(), f);
|
||||
case Parameters::Str:
|
||||
fprintf(outputFile, "%s = %s", paramName.c_str(), s.c_str());
|
||||
case Parameters::Undef:
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
ParamList::iterator findInsertionPoint(ParamList& paramList,
|
||||
const string& paramName)
|
||||
{
|
||||
unsigned short start = 0;
|
||||
unsigned short stop = paramList.size();
|
||||
while (stop != start) {
|
||||
unsigned short pos = start + (stop-start)/2;
|
||||
int comp = paramName.compare(paramList[pos].paramLabel());
|
||||
if (comp == 0)
|
||||
stop = start = pos;
|
||||
else if (comp > 0)
|
||||
start = pos + 1;
|
||||
else
|
||||
stop = pos;
|
||||
}
|
||||
|
||||
ParamList::iterator it=paramList.begin();
|
||||
it+=stop;
|
||||
return it;
|
||||
}
|
||||
|
||||
Parameters::Parameters()
|
||||
{}
|
||||
|
||||
void Parameters::readParameters(istream& paramStream)
|
||||
{
|
||||
while (!paramStream.eof()) {
|
||||
string param;
|
||||
getline(paramStream, param);
|
||||
param = trim(param);
|
||||
string paramName = nextToken(param);
|
||||
|
||||
if (paramName.length() == 0) continue;
|
||||
|
||||
if (*(paramName.data()) == '#') continue;
|
||||
|
||||
updateParameter(paramName, param.c_str());
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
bool Parameters::empty() {
|
||||
return paramList.empty();
|
||||
}
|
||||
|
||||
void Parameters::addParameter(const string& paramName, const int value)
|
||||
{
|
||||
ParamList::iterator pos = findInsertionPoint(paramList, paramName);
|
||||
if (pos != paramList.end() && (*pos).paramLabel() == paramName)
|
||||
(*pos) = Parameter(paramName, value);
|
||||
else
|
||||
paramList.insert(pos, Parameter(paramName, value));
|
||||
}
|
||||
|
||||
void Parameters::addParameter(const string& paramName, const double value)
|
||||
{
|
||||
ParamList::iterator pos = findInsertionPoint(paramList, paramName);
|
||||
if (pos != paramList.end() && (*pos).paramLabel() == paramName)
|
||||
(*pos) = Parameter(paramName, (float)value);
|
||||
else
|
||||
paramList.insert(pos, Parameter(paramName, (float)value));
|
||||
}
|
||||
|
||||
void Parameters::addParameter(const string& paramName, const string& value)
|
||||
{
|
||||
ParamList::iterator pos = findInsertionPoint(paramList, paramName);
|
||||
if (pos != paramList.end() && (*pos).paramLabel() == paramName)
|
||||
(*pos) = Parameter(paramName, value);
|
||||
else
|
||||
paramList.insert(pos, Parameter(paramName, value));
|
||||
}
|
||||
|
||||
void Parameters::updateParameter(const string& paramName,
|
||||
const char* const value)
|
||||
{
|
||||
ParamList::iterator pos = findInsertionPoint(paramList, paramName);
|
||||
if (pos != paramList.end() && (*pos).paramLabel() == paramName)
|
||||
switch ((*pos).paramType()) {
|
||||
case Int:
|
||||
(*pos) = Parameter(paramName, atoi(value));
|
||||
break;
|
||||
case Float:
|
||||
(*pos) = Parameter(paramName, (float)atof(value));
|
||||
break;
|
||||
case Str:
|
||||
(*pos) = Parameter(paramName, string(value));
|
||||
case Undef:
|
||||
(*pos) = Parameter(paramName, string(value));
|
||||
}
|
||||
else
|
||||
paramList.insert(pos, Parameter(paramName, string(value)));
|
||||
}
|
||||
|
||||
|
||||
ParamType Parameters::paramType(const string& paramName)
|
||||
{
|
||||
ParamList::iterator pos = findInsertionPoint(paramList, paramName);
|
||||
if (pos != paramList.end() && (*pos).paramLabel() == paramName)
|
||||
return (*pos).paramType();
|
||||
else
|
||||
return Undef;
|
||||
}
|
||||
|
||||
|
||||
int Parameters::getInt(const string& paramName, const int& defaultValue)
|
||||
{
|
||||
ParamList::iterator pos = findInsertionPoint(paramList, paramName);
|
||||
if (pos != paramList.end() && (*pos).paramLabel() == paramName)
|
||||
switch ((*pos).paramType()) {
|
||||
case Int:
|
||||
return (*pos).intValue();
|
||||
case Float:
|
||||
return (int)(*pos).floatValue();
|
||||
case Str:
|
||||
return atoi((*pos).stringValue().data());
|
||||
case Undef:
|
||||
break;
|
||||
}
|
||||
return defaultValue;
|
||||
}
|
||||
|
||||
float Parameters::getFloat(const string& paramName, const float& defaultValue)
|
||||
{
|
||||
ParamList::iterator pos = findInsertionPoint(paramList, paramName);
|
||||
if (pos != paramList.end() && (*pos).paramLabel() == paramName)
|
||||
switch ((*pos).paramType()) {
|
||||
case Float:
|
||||
return (*pos).floatValue();
|
||||
case Int:
|
||||
return (float)(*pos).intValue();
|
||||
case Str:
|
||||
return (float) atof((*pos).stringValue().data());
|
||||
case Undef:
|
||||
break;
|
||||
}
|
||||
return defaultValue;
|
||||
}
|
||||
|
||||
string Parameters::getString(const string& paramName,const string& defaultValue)
|
||||
{
|
||||
ParamList::iterator pos = findInsertionPoint(paramList, paramName);
|
||||
if (pos != paramList.end() && (*pos).paramLabel() == paramName)
|
||||
switch ((*pos).paramType()) {
|
||||
case Str:
|
||||
return (*pos).stringValue();
|
||||
case Float: {
|
||||
return appendDouble2string((*pos).floatValue());
|
||||
}
|
||||
case Int: {
|
||||
return appendInt2string((*pos).intValue());
|
||||
}
|
||||
case Undef:
|
||||
break;
|
||||
}
|
||||
return defaultValue;
|
||||
}
|
||||
|
||||
void Parameters::dump(ostream& out)
|
||||
{
|
||||
for (ParamList::iterator i=paramList.begin(); i != paramList.end(); ++i)
|
||||
out << *i << '\n';
|
||||
}
|
||||
|
||||
//void Parameters::dump(DebugStream& out, const unsigned int msgLevel)
|
||||
//{
|
||||
// for (ParamList::iterator i=paramList.begin(); i != paramList.end(); ++i)
|
||||
// out(msgLevel) << *i;
|
||||
//}
|
||||
|
||||
void Parameters::dump(FILE* outputFile) {
|
||||
for (ParamList::iterator i = paramList.begin() ; i != paramList.end() ; i++) {
|
||||
i->dump(outputFile);
|
||||
fprintf(outputFile, "\n");
|
||||
}
|
||||
|
||||
fprintf(outputFile, "\n");
|
||||
}
|
||||
|
||||
string Parameters::nextToken(string& str)
|
||||
{
|
||||
unsigned int start = 0;
|
||||
while (start < str.length() &&
|
||||
(str[start] == ' ' || str[start] == '\t' || str[start] == '\n'))
|
||||
++start;
|
||||
|
||||
if (start >= str.length()) {
|
||||
str = "";
|
||||
return "";
|
||||
}
|
||||
|
||||
unsigned int stop = start+1;
|
||||
while (stop < str.length() &&
|
||||
str[stop] != ' ' && str[stop] != '\t' && str[stop] != '\n')
|
||||
++stop;
|
||||
|
||||
unsigned int next = stop;
|
||||
while (next < str.length() &&
|
||||
(str[next] == ' ' || str[next] == '\t' || str[next] == '\n'))
|
||||
++next;
|
||||
|
||||
string result = str.substr((int)start, stop-start);
|
||||
str = str.substr((int)next);
|
||||
return result;
|
||||
}
|
||||
@ -1,251 +0,0 @@
|
||||
#ifndef _Parameters_h
|
||||
#define _Parameters_h
|
||||
|
||||
#include <iostream>
|
||||
#include <ostream>
|
||||
#include <string>
|
||||
#include <cstdlib>
|
||||
#include <cstdio>
|
||||
//#include "macros.h"
|
||||
//#include "DebugStream.h"
|
||||
//#include "StringUtils.h"
|
||||
|
||||
using std::string;
|
||||
using std::istream;
|
||||
using namespace std;
|
||||
|
||||
/*
|
||||
CLASS
|
||||
Parameters
|
||||
|
||||
A utility class used to manage program parameters. The class supports
|
||||
setting default values for parameters, reading values from a parameters
|
||||
file and accessing parameters values from other parts of the program.
|
||||
|
||||
KEYWORDS
|
||||
parameters
|
||||
|
||||
AUTHORS
|
||||
Meir Fuchs (mailto: meirfux@math.tau.ac.il)
|
||||
|
||||
Copyright: SAMBA group, Tel-Aviv Univ. Israel, 1997.
|
||||
|
||||
CHANGES LOG
|
||||
<UL>
|
||||
<LI>9.01.05 Dina:
|
||||
Bug fix: adding check to iterator end() to findInsertionPoint result
|
||||
to paramType, getInt, getString, getFloat functions
|
||||
</LI>
|
||||
<LI>17.05.04 Oranit Dror:
|
||||
Adding new methods: dump() and empty()
|
||||
</LI>
|
||||
</UL>
|
||||
|
||||
GOALS
|
||||
Aid in managing program parameters. The Parameters class's main goal is to
|
||||
relieve programmers from the need to rewrite specialized parameters reading
|
||||
code sections for each of the programs. The Parameters class holds integer,
|
||||
floating point or string values in static storage indexed using the
|
||||
parameter's name. Class also supplies method for parsing strings.
|
||||
|
||||
USAGE
|
||||
The following section covers several issues regarding the Parameters class
|
||||
and its usage. Users should understand the issues covered below before
|
||||
using the class.
|
||||
|
||||
USAGE: SETTING DEFAULT PARAMETERS
|
||||
Default parameters are set using the addParameter methods. Note that the
|
||||
type of the parameter is set according to the addParameter arguments. If
|
||||
a parameter is set using addParameter with an integer argument then
|
||||
subsequent updates (using updateParameter) to the same parameter will all
|
||||
be stored as integers. Therefore the following code should output a 0:
|
||||
EXAMPLE
|
||||
Parameters::addParameter("Dummy", 3);
|
||||
Parameters::updateParameter("Dummy", "This should set it to zero");
|
||||
cout << Parameters::getstring("Dummy");
|
||||
END
|
||||
|
||||
Note also that when setting defuault values of float parameters always use
|
||||
a decimal point or else these parameters will be added as intgers. For
|
||||
example:
|
||||
EXAMPLE
|
||||
Parameters::addParameter("CubeSize", 1.0); OK
|
||||
Parameters::addParameter("CubeSize", 1); Not OK. Integer parameter
|
||||
END
|
||||
|
||||
USAGE: READING PARAMETERS FROM FILE
|
||||
The readParameters method recieves an input stream from which parameters are
|
||||
to be read. Files are structured so that each line specifies the value of a
|
||||
parameter. Each line gives the parameter name, a white space and then the
|
||||
parameter value. Lines whose first non white-space charachter is # are
|
||||
ignored. A basic schema for using the Parameters class is to set the default
|
||||
values using addParameter calls and then calling readParameters to read in
|
||||
parameters with other values or new parameters. The following example works
|
||||
as such using the Parameters::dump method to print all the parameters
|
||||
and their values:
|
||||
EXAMPLE
|
||||
Parameters::addParameter("CubeSize", 1.0);
|
||||
Parameters::addParameter("MinVote", 8);
|
||||
ifstream params("params");
|
||||
Parameters::readParameters(params);
|
||||
params.close();
|
||||
Parameters::dump(cout);
|
||||
END
|
||||
With the following parameters file:
|
||||
EXAMPLE
|
||||
CubeSize 0.5
|
||||
File pdb4hhb.ent
|
||||
END
|
||||
The following output should result:
|
||||
EXAMPLE
|
||||
CubeSize (Float) 0.5
|
||||
File (Str) pdb4hhb.ent
|
||||
MinVote (Int) 8
|
||||
END
|
||||
|
||||
USAGE: ACCESSING PARAMETERS VALUES
|
||||
using the getInt, getFloat and getstring methods one may access the
|
||||
parameters values. Note that a value will always be returned even if the
|
||||
parameter is not stored as the same type. The get methods attempt to
|
||||
convert the parameter type to the requested return type of the method.
|
||||
The follwing code should produce 3 1's as its output:
|
||||
EXAMPLE:
|
||||
Parameters::addParameter("MaxMix", 1); OK added an integer parameter
|
||||
cout << Parameters::getInt("MaxMix");
|
||||
cout << Parameters::getFloat("MaxMix");
|
||||
cout << Parameters::getstring("MaxMix");
|
||||
END
|
||||
Also note that parameters names are case sensitive.
|
||||
|
||||
USAGE: SUBCLASSING AND PERFORMANCE
|
||||
The Parameters engine keeps the parameters in a sorted list. Although
|
||||
finding a parameter and its value in this list is considerably fast most
|
||||
users will not want this overhead of searching for the parameter using
|
||||
string comparisons inside their main loops, as part of a code which can be
|
||||
executed a great number of times.
|
||||
The idea is to subclass the Parameters class and hold the values which
|
||||
require direct and fast access in seperate static variables. All parameters
|
||||
are accessed not throguh the getParameter methods but rather through
|
||||
specialized methods of the subclass. The following is an example of such an
|
||||
implementation. Notice the readParameters method.
|
||||
EXAMPLE:
|
||||
static int min_vote = 8; // Default values
|
||||
static float cube_size = 1.0;
|
||||
|
||||
class ProgParams : protected Parameters
|
||||
{
|
||||
int minVote() { return min_vote };
|
||||
|
||||
float cubeSize() { return cube_size };
|
||||
|
||||
// file name is not held in static variable. Don't care about parameter
|
||||
// access time.
|
||||
string fileName() { return getstring("FileName"); }
|
||||
|
||||
int readParameters(char* paramsfile) {
|
||||
addParameter("MinVote", min_vote);
|
||||
addParameter("CubeSize", cube_size);
|
||||
|
||||
ifstream params(paramsfile);
|
||||
Parameters::readParameters(params);
|
||||
params.close();
|
||||
|
||||
min_vote = getInt("MinVote");
|
||||
cube_size = getFloat("CubeSize");
|
||||
}
|
||||
}
|
||||
END
|
||||
*/
|
||||
class Parameters
|
||||
{
|
||||
public:
|
||||
//// Used by the paramType method. See below.
|
||||
enum ParamType { Undef, Int, Float, Str };
|
||||
|
||||
//// readParameters recieves an input stream and reads parameters off this
|
||||
// input stream. See the usage section for details of how a parameters
|
||||
// file may be structured.
|
||||
static void readParameters(istream& paramStream);
|
||||
|
||||
////
|
||||
// Returns true if no parameters are defined. <br>
|
||||
// Author: Oranit Dror (oranit@tau.ac.il)
|
||||
static bool empty();
|
||||
|
||||
// GROUP: Setting parameters
|
||||
|
||||
//// Adds an integer parameter. The integer value added will actually be
|
||||
// stored as an integer. Subsequent updates to the same parameter using
|
||||
// updateParameter will all be stored as integers.
|
||||
static void addParameter(const string& paramName, const int value);
|
||||
|
||||
//// Adds a float parameter. The float value added will actually be
|
||||
// stored as a float. Subsequent updates to the same parameter using
|
||||
// updateParameter will all be stored as floats.
|
||||
static void addParameter(const string& paramName, const double value);
|
||||
|
||||
//// Adds a string parameter. The string value added will actually be
|
||||
// stored as a string. Subsequent updates to the same parameter using
|
||||
// updateParameter will all be stored as strings.
|
||||
static void addParameter(const string& paramName, const string& value);
|
||||
|
||||
//// Update the parameter value without changing the parameter type. The
|
||||
// value parameter is converted to the parameter's type if this parameter
|
||||
// already exists. If the parameter is not yet listed then updateParameter
|
||||
// adds a new parameter of string type.
|
||||
static void updateParameter(const string& paramName,
|
||||
const char* const value);
|
||||
|
||||
// GROUP: Getting parameters values.
|
||||
|
||||
//// Returns the storage type of the given parameter. If a parameter
|
||||
// of the given name does not exist then Undef is returned. See enum
|
||||
// ParamType above for possible return values.
|
||||
static ParamType paramType(const string& paramName);
|
||||
|
||||
//// Gets the integer value of a given parameter. If parameter is not of
|
||||
// integer type then its value is converted to integer. If parameter does
|
||||
// not exist a 0 is returned.
|
||||
static int getInt(const string& paramName, const int& defaultValue=0);
|
||||
|
||||
//// Gets the float value of a given parameter. If parameter is not of
|
||||
// float type then its value is converted to float. If parameter does
|
||||
// not exist a 0 is returned.
|
||||
static float getFloat(const string& paramName, const float& defaultValue=0.0);
|
||||
|
||||
//// Gets the string value of a given parameter. If parameter is not of
|
||||
// string type then its value is converted to string. If parameter does
|
||||
// not exist an empty string is returned.
|
||||
static string getString(const string& paramName, const string& defaultValue=string());
|
||||
|
||||
// GROUP: Other methods
|
||||
|
||||
|
||||
|
||||
//// Output all listed parameters. Used for debugging.
|
||||
static void dump(ostream& out);
|
||||
|
||||
//// Output all listed parameters. Used for debugging.
|
||||
//static void dump(DebugStream& out, const unsigned int msgLevel);
|
||||
|
||||
////
|
||||
// Output all listed parameters. <br>
|
||||
// Author: Oranit Dror (oranit@tau.ac.il)
|
||||
static void dump(FILE* outputFile);
|
||||
|
||||
//// A utility method. nextToken recieves an argument string, finds the first
|
||||
// white-space delimited token in this string and returns it while cutting
|
||||
// this token off of the argument string (It it passed by reference). Tokens
|
||||
// are returned without any spaces. This method may be used repetitively to
|
||||
// tokenize a string.
|
||||
static string nextToken(string& str);
|
||||
|
||||
protected:
|
||||
//// Constructor is protected since all methods are static. No need to
|
||||
// actually form an instance of this class.
|
||||
Parameters();
|
||||
};
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
Binary file not shown.
@ -1,7 +0,0 @@
|
||||
// $Id: aaJC.cpp 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#include "aaJC.h"
|
||||
#include "errorMsg.h"
|
||||
|
||||
|
||||
|
||||
@ -1,52 +0,0 @@
|
||||
// $Id: aaJC.h 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#ifndef ___AA_JC
|
||||
#define ___AA_JC
|
||||
|
||||
#include "replacementModel.h"
|
||||
#include <cmath>
|
||||
using namespace std;
|
||||
|
||||
namespace aaDef {
|
||||
const MDOUBLE Alp = 20.0;
|
||||
const MDOUBLE odAl = 1.0/Alp; // one divided by alphabet
|
||||
const MDOUBLE om_odAl = 1.0-odAl; // one minus odAl;
|
||||
const MDOUBLE alDiv_omalp = Alp/(Alp-1.0);
|
||||
const MDOUBLE m_alDiv_omalp = -alDiv_omalp;
|
||||
}
|
||||
|
||||
class aaJC : public replacementModel {
|
||||
public:
|
||||
|
||||
virtual replacementModel* clone() const { return new aaJC(*this); }// see note down:
|
||||
// virtual aaJC* clone() const { return new aaJC(*this); }
|
||||
const int alphabetSize() const {return 20;}
|
||||
|
||||
explicit aaJC(){};
|
||||
const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const {
|
||||
//(wrong!) return ((i==j) ? 0.05+0.95*exp(-20.0*d): 0.05-0.05*exp(-20.0*d));
|
||||
return ((i==j) ? aaDef::odAl+aaDef::om_odAl*exp(aaDef::m_alDiv_omalp*d): aaDef::odAl-aaDef::odAl*exp(aaDef::m_alDiv_omalp*d));
|
||||
|
||||
}
|
||||
|
||||
const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const{
|
||||
//(worng!)return ((i==j) ? -19.0*exp(-20.0*d): exp(-20.0*d));
|
||||
return ((i==j) ? -exp(aaDef::m_alDiv_omalp*d): exp(aaDef::m_alDiv_omalp*d)/(aaDef::Alp-1));
|
||||
}
|
||||
const MDOUBLE freq(const int i) const {return aaDef::odAl;};
|
||||
|
||||
const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const{
|
||||
//(wrong!) return ((i==j) ? 19.0*20.0*exp(-20.0*d): 0.0-20.0*exp(-20.0*d));
|
||||
return ((i==j) ? aaDef::alDiv_omalp*exp(aaDef::m_alDiv_omalp*d): aaDef::m_alDiv_omalp*exp(aaDef::m_alDiv_omalp*d));
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
#endif
|
||||
|
||||
// note: according to the new C++ rules, the clone function should be like this:
|
||||
// virtual aaJC* clone() const { return new aaJC(*this); }
|
||||
// however, not all compiler support it yet. look at More Effective C++ page 126.
|
||||
|
||||
|
||||
|
||||
Binary file not shown.
@ -1,72 +0,0 @@
|
||||
" 634 "
|
||||
" 25105 560 "
|
||||
" 1209 37271 620 "
|
||||
" 1353 344 196 494 "
|
||||
" 112 2048 176 34 21460 "
|
||||
" 0 140 1656 380 71026 41523 "
|
||||
" 238 255 56 2967 35040 33972 43340 "
|
||||
" 8628 295 812 370 1546 65 0 23 "
|
||||
" 328 7142 272 370 715 4680 1286 876 707 "
|
||||
" 1192 289 7588 303 103 124 1929 82 52300 924 "
|
||||
" 509 0 304 10057 836 0 806 6124 1328 45060 1132 "
|
||||
" 607 43 47 105 5067 0 0 0 863 56 221 189 "
|
||||
" 0 301 43 0 0 2141 279 0 0 475 32 0 27331 "
|
||||
" 167 88 393 141 1487 366 3364 545 193 140 538 162 5087 1030 "
|
||||
" 34 0 42 421 0 0 346 3233 0 0 61 718 31469 35230 1626 "
|
||||
" 2841 308 69 647 711 76 0 346 1297 278 124 413 193 49 200 0 "
|
||||
" 195 2491 229 114 57 356 73 12 114 945 197 0 8 74 42 9 2449 "
|
||||
" 286 295 1514 350 199 128 640 63 66 257 565 175 42 15 241 41 31892 2201 "
|
||||
" 352 19 175 3379 195 32 0 441 246 85 129 1259 106 0 126 176 4155 62775 2262 "
|
||||
" 190 36 58 114 2112 0 0 0 0 51 81 158 201 0 114 51 2926 203 490 116 "
|
||||
" 37 204 30 71 0 1701 355 109 35 444 1 0 27 114 56 21 205 1284 335 79 21842 "
|
||||
" 81 99 218 95 183 0 4067 30 94 182 10 76 164 61 192 0 617 512 2569 361 57041 44793 "
|
||||
" 54 30 30 239 134 158 0 2062 10 30 35 370 101 0 70 141 263 0 183 1574 32490 33996 32457 "
|
||||
" 1891 0 623 93 0 147 671 0 46674 151 12628 0 11 0 0 134 8237 543 0 277 818 47 0 0 "
|
||||
" 701 549 1184 0 0 246 241 87 5836 1540 12311 0 6 41 48 0 452 5598 739 0 16 841 253 0 40388 "
|
||||
" 854 120 2602 57 54 69 359 0 13337 47 37725 91 0 31 105 0 0 660 5014 399 118 0 2656 0 82443 40802 "
|
||||
" 695 0 735 893 81 28 0 661 12916 0 6008 2384 89 35 60 56 1344 0 484 9142 0 0 0 1483 85032 87710 53112 "
|
||||
" 208 39 0 46 600 0 0 0 19 0 0 55 7884 0 1512 386 2427 200 95 0 3069 0 0 0 2011 0 15 0 "
|
||||
" 35 133 6 0 0 387 59 0 0 142 42 0 365 3634 769 272 79 813 191 114 0 1470 0 70 95 1012 0 0 17551 "
|
||||
" 0 15 74 0 97 91 378 52 27 44 46 8 876 732 2298 588 106 83 604 90 286 0 1947 0 0 70 707 0 33878 14863 "
|
||||
" 63 0 14 229 8 0 114 484 67 48 0 147 280 278 720 3849 349 0 160 1407 0 0 0 1951 0 3 43 1427 22703 32337 15002 "
|
||||
" 1304 155 0 389 408 75 0 79 444 170 0 236 197 11 45 0 2595 59 234 256 149 35 74 60 51 0 0 143 109 12 0 27 "
|
||||
" 120 2602 73 69 0 258 160 112 46 821 22 78 0 43 18 0 158 647 151 46 14 149 84 17 1 119 23 2 0 42 7 20 2320 "
|
||||
" 0 168 893 221 158 73 415 109 0 180 336 209 35 1 131 44 138 148 1538 143 107 83 168 39 1 91 217 0 0 26 55 14 23280 3052 "
|
||||
" 117 9 91 3406 173 5 0 311 55 62 40 1017 39 0 16 75 274 0 113 787 57 14 76 93 0 16 26 138 10 0 1 44 3660 28072 2533 "
|
||||
" 450 59 100 310 7741 0 0 0 225 220 182 557 1008 0 588 153 639 41 127 145 2469 39 211 190 150 0 48 78 625 0 97 61 1324 82 245 122 "
|
||||
" 28 466 94 52 0 6013 75 0 50 1265 106 0 0 452 240 0 47 248 183 0 14 2010 303 164 55 277 0 61 0 333 64 62 86 670 189 0 17008 "
|
||||
" 130 336 356 168 0 401 16072 0 103 537 357 370 656 161 817 0 379 93 512 228 0 428 10166 0 0 195 789 0 0 83 543 33 0 379 1907 42 47381 29661 "
|
||||
" 89 80 65 525 0 0 0 7268 98 211 0 1307 86 67 226 484 125 11 108 230 58 130 0 2312 0 0 130 252 29 17 64 381 133 0 145 799 30850 26704 28871 "
|
||||
" 285 65 23 253 446 24 106 6 2230 278 0 315 177 0 65 33 468 34 17 54 163 23 55 33 366 0 0 0 145 26 0 28 1661 180 0 104 2231 92 0 278 "
|
||||
" 28 1227 58 189 12 521 129 103 53 5470 0 0 37 87 33 21 31 344 83 26 64 236 268 30 0 941 162 1 0 80 13 28 0 1655 105 0 0 2186 744 149 19297 "
|
||||
" 27 356 299 139 176 0 843 160 0 684 3262 829 29 45 241 0 110 65 309 60 76 115 522 18 0 0 1073 0 0 2 82 0 0 67 1559 183 750 315 5134 73 44365 23295 "
|
||||
" 92 205 66 1727 96 190 0 728 0 13 0 7147 0 0 47 96 0 0 89 555 60 34 0 335 244 0 0 1432 18 0 18 105 59 0 63 2203 356 0 0 2632 28434 37047 23095 "
|
||||
" 318 54 33 115 3527 41 76 0 518 181 0 64 23970 0 1303 260 576 75 64 47 821 131 0 0 179 0 0 0 4505 11 14 274 764 39 80 51 6746 0 0 30 1310 0 179 0 "
|
||||
" 27 179 23 44 3 2249 0 308 11 354 78 34 330 12669 395 164 61 157 53 32 75 413 144 0 0 108 75 38 251 3338 87 38 51 294 54 0 0 4666 0 0 0 797 0 0 22326 "
|
||||
" 20 26 113 25 429 137 2071 322 0 22 220 58 3262 1931 2537 1548 21 38 128 48 121 44 321 57 0 41 121 25 34 50 1723 0 34 0 336 11 1230 167 5933 77 0 0 790 43 45141 19340 "
|
||||
" 76 42 6 207 135 150 294 2554 64 143 0 486 810 110 539 13791 171 2 57 142 0 0 134 537 0 31 5 200 0 58 22 3459 129 0 7 388 0 0 0 5346 0 31 0 1160 31707 35610 22203 "
|
||||
" 18 407 23 0 0 68 19 36 42 165 0 0 2 88 44 2 117 3381 122 0 0 99 45 6 0 290 36 0 0 266 30 38 18 159 13 0 1 58 142 23 0 80 5 0 3 144 35 0 "
|
||||
" 33 0 23 658 24 44 108 126 0 20 64 327 60 14 66 133 254 286 87 4548 15 0 8 90 141 9 0 754 142 1 81 288 33 0 33 255 39 24 0 112 18 0 29 130 37 14 20 166 53555 "
|
||||
" 277 164 108 290 6514 235 482 1018 165 446 8 1100 435 12 319 0 838 111 227 157 5890 0 507 0 340 0 64 3 320 0 0 0 245 73 90 109 6631 419 0 627 412 59 338 125 825 102 176 201 47 59 "
|
||||
" 51 577 50 66 169 4821 1421 355 54 2047 24 106 112 72 80 62 188 439 166 46 0 5279 0 0 0 368 104 23 0 445 72 0 30 239 87 0 264 4869 738 374 122 466 103 38 4 415 40 126 541 37 22923 "
|
||||
" 110 82 145 163 1203 0 14459 754 24 1451 151 763 183 30 477 38 0 233 599 0 273 0 12183 0 111 219 802 0 707 0 0 0 110 158 176 42 520 675 20335 0 0 499 1107 178 0 0 564 0 146 0 76141 40261 "
|
||||
" 112 181 54 602 1180 581 0 5578 112 651 68 1954 0 31 157 150 297 90 115 657 0 135 0 5714 0 0 0 679 0 0 41 578 87 3 74 288 631 521 937 5109 167 107 21 611 147 31 96 454 0 834 31553 32600 44414 "
|
||||
" 31 241 33 0 45 319 0 86 16 1649 42 219 33 130 46 2 125 576 73 12 0 102 64 24 110 1890 226 0 0 317 18 43 0 51 24 0 56 410 279 66 0 774 82 0 50 219 33 124 1297 0 172 1595 327 77 "
|
||||
" 20 14 49 22 39 18 92 0 48 39 549 56 30 14 95 20 79 42 201 130 28 0 142 1 270 84 1199 29 74 19 105 19 10 3 27 6 35 31 67 0 8 14 446 0 13 9 56 41 166 229 174 47 576 33 341 "
|
||||
" 43 8 28 397 156 20 280 403 108 352 75 2043 29 21 59 187 145 43 89 989 22 0 91 211 106 0 104 2711 123 20 35 305 27 19 7 86 180 46 200 423 72 80 88 1072 108 58 112 224 0 2135 495 0 187 2090 61046 387 "
|
||||
" 123 9 9 101 615 6 102 140 180 69 106 0 6752 231 1116 418 193 9 104 167 205 38 23 15 0 83 4 103 54777 7485 8703 8464 67 34 41 0 611 88 0 90 49 0 18 92 6666 153 0 364 159 265 4644 80 0 186 96 51 168 "
|
||||
" 12 70 0 0 23 155 11 48 3 70 0 0 70 742 186 61 38 346 27 46 25 170 6 0 0 117 17 14 220 2693 284 0 5 27 8 0 0 162 124 20 3 48 23 0 28 957 87 0 3979 750 23 924 0 0 574 154 61 1268 "
|
||||
" 59 45 80 75 192 81 637 163 28 0 74 99 1733 57 3345 832 131 42 198 55 181 6 226 149 53 0 94 204 14044 5603 27723 9664 97 0 37 34 172 50 1000 141 1 32 254 0 523 72 2117 491 102 84 1377 107 5207 276 111 744 201 47609 814 "
|
||||
" 9 17 12 85 47 14 107 170 21 21 26 101 326 48 262 910 73 74 23 359 0 0 55 201 17 0 20 146 234 0 387 2714 16 0 5 30 82 2 39 186 30 18 5 66 172 13 125 928 625 4904 160 0 206 991 125 212 787 1638 32469 1494 "
|
||||
" 0.0282483 0.0206292 0.0319075 0.0182494 0.0168831 0.0159757 0.0058938 0.0144022 0.0135116 0.0190724 0.0118542 0.0136325 0.0093705 0.0199714 0.0218874 0.0174818 "
|
||||
" 0.0136792 0.0143825 0.0337043 0.0116006 0.0177685 0.0150006 0.0058835 0.0176118 0.0061893 0.0087184 0.0084944 0.0054224 0.0080368 0.0173529 0.0373569 0.0150280 "
|
||||
" 0.0311168 0.0246045 0.0388972 0.0251865 0.0179100 0.0212765 0.0059683 0.0199671 0.0184506 0.0176209 0.0132786 0.0115579 0.0083782 0.0137699 0.0265260 0.0136025 "
|
||||
" 0.0159995 0.0132055 0.0133496 0.0159777 0.0043280 0.0171276 0.0119089 0.0124708 0.0109899 0.0085271 0.0195872 0.0141357 0.0190797 "
|
||||
" AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT "
|
||||
" CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT "
|
||||
" GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT "
|
||||
" TAC TAT TCA TCC TCG TCT TGC TGG TGT TTA TTC TTG TTT "
|
||||
" S_ij = S_ji and PI_i based on the empirical codon matrix: "
|
||||
" A Schneider, GM Cannarozzi and GH Gonnet. Empirical codon "
|
||||
" substitution matrix. BMC Bioinformatics 6:134. 2005. "
|
||||
|
||||
@ -1,134 +0,0 @@
|
||||
// $Id: allTrees.cpp 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#include "definitions.h"
|
||||
#include "allTrees.h"
|
||||
#include "treeUtil.h"
|
||||
#include "treeIt.h"
|
||||
#include "bblEM.h"
|
||||
#include <algorithm>
|
||||
#include <iostream>
|
||||
|
||||
#include "someUtil.h"
|
||||
|
||||
using namespace std;
|
||||
#ifndef VERBOS
|
||||
#define VERBOS
|
||||
#endif
|
||||
|
||||
|
||||
allTrees::allTrees(bool keepAllTrees) : _keepAllTrees(keepAllTrees) {
|
||||
_bestScore = VERYSMALL;
|
||||
}
|
||||
|
||||
void get3seqTreeAndIdLeftVec(const sequenceContainer* sc,
|
||||
tree& starT,
|
||||
vector<int>& idList){
|
||||
sequenceContainer::constTaxaIterator tIt;
|
||||
sequenceContainer::constTaxaIterator tItEnd;
|
||||
tIt.begin(*sc);
|
||||
tItEnd.end(*sc);
|
||||
while(tIt != tItEnd) {
|
||||
idList.push_back(tIt->id());
|
||||
++tIt;
|
||||
}
|
||||
if (sc->numberOfSeqs()<3) errorMsg::reportError(" searching a tree for number of sequences < 3 ");
|
||||
starT.createRootNode();
|
||||
starT.createNode(starT.getRoot(),1);
|
||||
starT.createNode(starT.getRoot(),2);
|
||||
starT.createNode(starT.getRoot(),3);
|
||||
|
||||
const string nameOfSeq1 = (*sc)[idList[idList.size()-1]].name();
|
||||
const string nameOfSeq2 = (*sc)[idList[idList.size()-2]].name();
|
||||
const string nameOfSeq3 = (*sc)[idList[idList.size()-3]].name();
|
||||
idList.pop_back();
|
||||
idList.pop_back();
|
||||
idList.pop_back();
|
||||
|
||||
starT.getRoot()->getSon(0)->setName(nameOfSeq1);
|
||||
starT.getRoot()->getSon(1)->setName(nameOfSeq2);
|
||||
starT.getRoot()->getSon(2)->setName(nameOfSeq3);
|
||||
starT.createFlatLengthMatrix();
|
||||
}
|
||||
|
||||
void allTrees::recursiveFind( const sequenceContainer* sc,
|
||||
const stochasticProcess* sp,
|
||||
const Vdouble * weights,
|
||||
const int maxIterations,
|
||||
const MDOUBLE epsilon){
|
||||
tree starT;
|
||||
vector<int> ids;
|
||||
get3seqTreeAndIdLeftVec(sc,starT,ids);
|
||||
recursiveFind(starT,*sp,*sc,ids,weights,maxIterations,epsilon);
|
||||
}
|
||||
|
||||
tree getAnewTreeFrom(const tree& et, tree::nodeP & mynode,
|
||||
vector<int> & idLeft, const string& nameToAdd) {
|
||||
tree newT = et;
|
||||
tree::nodeP mynodeInNewTree = newT.findNodeByName(mynode->name());
|
||||
// int NameToAdd = idLeft[idLeft.size()-1];
|
||||
idLeft.pop_back();
|
||||
tree::nodeP fatherNode = mynodeInNewTree->father();
|
||||
tree::nodeP newInternalNode = newT.createNode(fatherNode, newT.getNodesNum());
|
||||
mynodeInNewTree->setFather(newInternalNode);
|
||||
newInternalNode->setSon(mynodeInNewTree);
|
||||
|
||||
fatherNode->removeSon(mynodeInNewTree);
|
||||
tree::nodeP newOTU= newT.createNode(newInternalNode, newT.getNodesNum());;
|
||||
//string nameX = (*sc)[NameToAdd].name();
|
||||
newOTU->setName(nameToAdd);
|
||||
newOTU->setDisToFather(tree::FLAT_LENGTH_VALUE);
|
||||
newInternalNode->setDisToFather(tree::FLAT_LENGTH_VALUE);
|
||||
newT.create_names_to_internal_nodes();
|
||||
|
||||
return newT;
|
||||
}
|
||||
|
||||
void allTrees::recursiveFind(tree et,
|
||||
const stochasticProcess& sp,
|
||||
const sequenceContainer& sc,
|
||||
vector<int> idLeft,
|
||||
const Vdouble * weights,
|
||||
const int maxIterations,
|
||||
const MDOUBLE epsilon) {
|
||||
|
||||
if (idLeft.empty()) {
|
||||
//static int k=1; k++;
|
||||
MDOUBLE treeScore = evalTree(et,sp,sc,maxIterations,epsilon,weights);
|
||||
if (_keepAllTrees) {
|
||||
_allPossibleTrees.push_back(et);
|
||||
_allPossibleScores.push_back(treeScore);
|
||||
}
|
||||
LOG(5,<<".");
|
||||
//LOG(5,<<"tree: "<<k<<" l= "<<treeScore<<endl);
|
||||
if (treeScore > _bestScore) {
|
||||
//LOG(5,<<"new Best score!"<<endl);
|
||||
_bestTree = et;
|
||||
_bestScore = treeScore;
|
||||
}
|
||||
} else {
|
||||
treeIterTopDown tIt(et);
|
||||
tree::nodeP mynode = tIt.first();
|
||||
mynode = tIt.next(); // skipping the root
|
||||
for (; mynode != tIt.end(); mynode = tIt.next()) {
|
||||
int NameToAdd = idLeft[idLeft.size()-1];
|
||||
tree newT = getAnewTreeFrom(et,mynode,idLeft,sc[NameToAdd].name());
|
||||
recursiveFind(newT,sp,sc,idLeft,weights,maxIterations,epsilon);
|
||||
idLeft.push_back(NameToAdd);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
MDOUBLE allTrees::evalTree( tree& et,
|
||||
const stochasticProcess& sp,
|
||||
const sequenceContainer& sc,
|
||||
const int maxIterations,
|
||||
const MDOUBLE epsilon,
|
||||
const Vdouble * weights) {
|
||||
bblEM bblEM1(et,sc,sp,weights,maxIterations,epsilon);
|
||||
MDOUBLE res =bblEM1.getTreeLikelihood();
|
||||
return res;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,68 +0,0 @@
|
||||
// $Id: allTrees.h 1731 2007-02-26 13:45:23Z itaymay $
|
||||
|
||||
#ifndef ___ALL_TREES
|
||||
#define ___ALL_TREES
|
||||
|
||||
#include "definitions.h"
|
||||
#include "tree.h"
|
||||
#include "sequenceContainer.h"
|
||||
#include "stochasticProcess.h"
|
||||
#include <vector>
|
||||
using namespace std;
|
||||
|
||||
void get3seqTreeAndIdLeftVec(const sequenceContainer* sc,
|
||||
tree& starT,
|
||||
vector<int>& idList);
|
||||
|
||||
tree getAnewTreeFrom( const tree& et,
|
||||
tree::nodeP & mynode,
|
||||
vector<int> & idLeft,
|
||||
const string& nameToAdd);
|
||||
class allTrees {
|
||||
public:
|
||||
explicit allTrees(bool keepAllTrees = false);
|
||||
MDOUBLE getBestScore() {return _bestScore;}
|
||||
tree getBestTree() {return _bestTree;}
|
||||
|
||||
void getAllTreesAndLikelihoods(vector<tree>& resTree,VdoubleRep & scores) {
|
||||
resTree = _allPossibleTrees;
|
||||
scores = _allPossibleScores;
|
||||
}
|
||||
|
||||
void recursiveFind( tree et,
|
||||
const stochasticProcess& sp,
|
||||
const sequenceContainer& sc,
|
||||
vector<int> idLeft,
|
||||
const Vdouble * weights = NULL,
|
||||
const int maxIterations=1000,
|
||||
const MDOUBLE epsilon=0.05);
|
||||
|
||||
void recursiveFind( const sequenceContainer* sc,
|
||||
const stochasticProcess* sp,
|
||||
const Vdouble * weights = NULL,
|
||||
const int maxIterations=1000,
|
||||
const MDOUBLE epsilon=0.05); // one tree.
|
||||
|
||||
|
||||
|
||||
private:
|
||||
tree _bestTree;
|
||||
MDOUBLE _bestScore;
|
||||
vector<tree> _allPossibleTrees;
|
||||
vector<doubleRep> _allPossibleScores;
|
||||
const bool _keepAllTrees;
|
||||
|
||||
|
||||
MDOUBLE evalTree(tree& et,
|
||||
const stochasticProcess& sp,
|
||||
const sequenceContainer& sc,
|
||||
const int maxIterations,
|
||||
const MDOUBLE epsilon,
|
||||
const Vdouble * weights = NULL);
|
||||
|
||||
|
||||
|
||||
|
||||
};
|
||||
#endif
|
||||
|
||||
Binary file not shown.
@ -1,83 +0,0 @@
|
||||
// $Id: allTreesSeparateModel.cpp 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#include "definitions.h"
|
||||
#include "treeIt.h"
|
||||
#include "allTreesSeparateModel.h"
|
||||
#include "bblEMSeperate.h"
|
||||
#include <algorithm>
|
||||
#include <iostream>
|
||||
|
||||
#include "someUtil.h"
|
||||
|
||||
using namespace std;
|
||||
#ifndef VERBOS
|
||||
#define VERBOS
|
||||
#endif
|
||||
|
||||
|
||||
allTreesSeparateModel::allTreesSeparateModel(){
|
||||
_bestScore = VERYSMALL;
|
||||
}
|
||||
|
||||
void allTreesSeparateModel::recursiveFind( const vector<sequenceContainer>* sc,
|
||||
const vector<stochasticProcess>* sp,
|
||||
const vector<Vdouble* > * weights,
|
||||
const int maxIterations,
|
||||
const MDOUBLE epsilon){
|
||||
tree starT;
|
||||
vector<int> ids;
|
||||
get3seqTreeAndIdLeftVec(&(*sc)[0],starT,ids);
|
||||
recursiveFind(starT,*sp,*sc,ids,weights,maxIterations,epsilon);
|
||||
}
|
||||
|
||||
void allTreesSeparateModel::recursiveFind(tree et,
|
||||
const vector<stochasticProcess>& sp,
|
||||
const vector<sequenceContainer>& sc,
|
||||
vector<int> idLeft,
|
||||
const vector<Vdouble* > * weights,
|
||||
const int maxIterations,
|
||||
const MDOUBLE epsilon) {
|
||||
|
||||
if (idLeft.empty()) {
|
||||
//static int k=1; k++;
|
||||
MDOUBLE treeScore = evalTree(et,sp,sc,maxIterations,epsilon,weights);
|
||||
//LOG(5,<<"tree: "<<k<<" l= "<<treeScore<<endl);
|
||||
LOG(5,<<".");
|
||||
if (treeScore > _bestScore) {
|
||||
//LOG(5,<<"new Best score!"<<endl);
|
||||
_bestTree = et;
|
||||
_bestScore = treeScore;
|
||||
_treeVecBest = _treeVecTmp; // keep the seperate trees too.
|
||||
}
|
||||
} else {
|
||||
et.create_names_to_internal_nodes();
|
||||
treeIterTopDown tIt(et);
|
||||
tree::nodeP mynode = tIt.first();
|
||||
mynode = tIt.next(); // skipping the root
|
||||
for (; mynode != tIt.end(); mynode = tIt.next()) {
|
||||
int NameToAdd = idLeft[idLeft.size()-1];
|
||||
tree newT = getAnewTreeFrom(et,mynode,idLeft,sc[0][NameToAdd].name());
|
||||
recursiveFind(newT,sp,sc,idLeft,weights,maxIterations,epsilon);
|
||||
idLeft.push_back(NameToAdd);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
MDOUBLE allTreesSeparateModel::evalTree( tree& et,
|
||||
const vector<stochasticProcess>& sp,
|
||||
const vector<sequenceContainer>& sc,
|
||||
const int maxIterations,
|
||||
const MDOUBLE epsilon,
|
||||
const vector<Vdouble* > * weights) {
|
||||
MDOUBLE res = 0;
|
||||
vector<tree> tVec;
|
||||
for (int k=0; k < sc.size(); ++k ) tVec.push_back(et);
|
||||
bblEMSeperate bblemsep1(tVec,sc,sp,weights,maxIterations,epsilon);
|
||||
res = bblemsep1.getTreeLikelihood();
|
||||
_treeVecTmp = tVec;
|
||||
return res;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,76 +0,0 @@
|
||||
// $Id: allTreesSeparateModel.h 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#ifndef ___ALL_TREES_SEPARATE_MODEL
|
||||
#define ___ALL_TREES_SEPARATE_MODEL
|
||||
|
||||
#include "definitions.h"
|
||||
#include "tree.h"
|
||||
#include "sequenceContainer.h"
|
||||
#include "stochasticProcess.h"
|
||||
#include <vector>
|
||||
using namespace std;
|
||||
|
||||
void get3seqTreeAndIdLeftVec(const sequenceContainer* sc,
|
||||
tree& starT,
|
||||
vector<int>& idList);
|
||||
|
||||
tree getAnewTreeFrom( const tree& et,
|
||||
tree::nodeP & mynode,
|
||||
vector<int> & idLeft,
|
||||
const string& nameToAdd);
|
||||
|
||||
|
||||
class allTreesSeparateModel {
|
||||
public:
|
||||
explicit allTreesSeparateModel();
|
||||
MDOUBLE getBestScore() {return _bestScore;}
|
||||
tree getBestTree() {return _bestTree;}
|
||||
|
||||
void recursiveFind(tree et,
|
||||
const vector<stochasticProcess>& sp,
|
||||
const vector<sequenceContainer>& sc,
|
||||
vector<int> idLeft,
|
||||
const vector<Vdouble* > * weights=NULL,
|
||||
const int maxIterations=1000,
|
||||
const MDOUBLE epsilon=0.05);
|
||||
|
||||
void recursiveFind( const vector<sequenceContainer>* sc,
|
||||
const vector<stochasticProcess>* sp,
|
||||
const vector<Vdouble* > * weights= NULL,
|
||||
const int maxIterations=1000,
|
||||
const MDOUBLE epsilon=0.05); // one tree.
|
||||
|
||||
vector<tree> getTreeVecBest() {return _treeVecBest;}
|
||||
|
||||
private:
|
||||
tree _bestTree;
|
||||
MDOUBLE _bestScore;
|
||||
vector<tree> _treeVecTmp; // same tree topologies, diff branch lengths
|
||||
vector<tree> _treeVecBest;// same tree topologies, diff branch lengths
|
||||
|
||||
|
||||
MDOUBLE evalTree( tree& et,
|
||||
const vector<stochasticProcess>& sp,
|
||||
const vector<sequenceContainer>& sc,
|
||||
const int maxIterations,
|
||||
const MDOUBLE epsilon,
|
||||
const vector<Vdouble* > * weights = NULL);
|
||||
|
||||
};
|
||||
#endif
|
||||
|
||||
// const stochasticProcess* _sp;
|
||||
//const sequenceContainer* _sc;
|
||||
//const Vdouble * _weights;
|
||||
|
||||
//vector<tree> getBestTreesSep() {return _bestSepTrees;}
|
||||
//vector<tree> _bestSepTrees;
|
||||
//vector<tree> _tmpSepTrees;
|
||||
//vector<tree> recursiveFindSep(const vector<sequenceContainer>* sc,
|
||||
// const vector<stochasticProcess>* sp,
|
||||
// const vector<Vdouble *> * weights,
|
||||
// const int maxIterations=1000,
|
||||
// const MDOUBLE epsilon=0.05); // sep model
|
||||
//const vector<sequenceContainer>* _scVec;
|
||||
//vector<stochasticProcess>* _spVec; // not const, so in proportional for example it can be changed.
|
||||
//const vector<Vdouble *> * _weightsVec;
|
||||
Binary file not shown.
@ -1,56 +0,0 @@
|
||||
// $Id: alphaTrivialAccelerator.h 962 2006-11-07 15:13:34Z privmane $
|
||||
|
||||
#ifndef ___ALPHA_TRIVIAL_ACCELERATOR
|
||||
#define ___ALPHA_TRIVIAL_ACCELERATOR
|
||||
|
||||
#include "pijAccelerator.h"
|
||||
#include "readDatMatrix.h"
|
||||
class alphaTrivialAccelerator : public pijAccelerator {
|
||||
public:
|
||||
|
||||
explicit alphaTrivialAccelerator(pupAll* pb, const MDOUBLE alpha) :
|
||||
_pb(static_cast<pupAll *> (pb->clone())),
|
||||
_alpha(alpha)
|
||||
{};
|
||||
|
||||
alphaTrivialAccelerator(const alphaTrivialAccelerator& other):
|
||||
_pb(NULL),
|
||||
_alpha(other._alpha) {
|
||||
if (other._pb != NULL)
|
||||
_pb = static_cast<pupAll *>(other._pb->clone());
|
||||
}
|
||||
|
||||
const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d) const {return _pb->Pij_tAlpha(i,j,d,_alpha);}
|
||||
|
||||
const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d) const{return _pb->Pij_tAlpha_dt(i,j,d,_alpha);};
|
||||
|
||||
const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d) const{return _pb->Pij_tAlpha_dt2(i,j,d,_alpha);};
|
||||
|
||||
const MDOUBLE Pij_t(const int i,const int j, const MDOUBLE d, const MDOUBLE alpha) const {return _pb->Pij_tAlpha(i,j,d,alpha);}
|
||||
|
||||
const MDOUBLE dPij_dt(const int i,const int j, const MDOUBLE d, const MDOUBLE alpha) const{return _pb->Pij_tAlpha_dt(i,j,d,alpha);};
|
||||
|
||||
const MDOUBLE d2Pij_dt2(const int i,const int j, const MDOUBLE d, const MDOUBLE alpha) const{return _pb->Pij_tAlpha_dt2(i,j,d,alpha);};
|
||||
|
||||
const MDOUBLE freq(const int i) const{return _pb->freq(i);}
|
||||
|
||||
virtual pijAccelerator* clone() const { return new alphaTrivialAccelerator(*this);}
|
||||
|
||||
virtual ~alphaTrivialAccelerator() {delete _pb;}
|
||||
|
||||
virtual const int alphabetSize() const {return _pb->alphabetSize();}
|
||||
|
||||
virtual replacementModel* getReplacementModel() const {
|
||||
return (static_cast<replacementModel * const>(_pb));
|
||||
}
|
||||
|
||||
const MDOUBLE alpha(void) const {return _alpha;}
|
||||
void setAlpha(const MDOUBLE alpha) {_alpha=alpha;}
|
||||
|
||||
private:
|
||||
pupAll* _pb;
|
||||
MDOUBLE _alpha;
|
||||
};
|
||||
|
||||
#endif
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Loading…
x
Reference in New Issue
Block a user