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v6.0

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• 035b8a61f0
  Update and rename Query_SRA_egs.py to QuerySRA_v1.0.py Godwin Ani 2024-01-15 15:05:23 -05:00
• fa44e2176c
  Update and rename get_unique_taxa.py to GetUniqueTaxa_v1.0.py Godwin Ani 2024-01-15 15:03:39 -05:00
• c1b32c97ae
  Update ReadMapping_v2.0.py Godwin Ani 2024-01-15 15:02:24 -05:00
• a63b2e7dd7
  Rename readmapping.py to ReadMapping_v2.0.py Godwin Ani 2024-01-15 15:01:33 -05:00
• dfa0f81763
  Update and rename rename_tip_labels.py to RenameTips_v1.0.py Godwin Ani 2024-01-15 15:00:53 -05:00
• a25d0ac289
  Rename CountTaxonOccurence.py to CountTaxonOccurence_v2.0.py Godwin Ani 2024-01-15 15:00:07 -05:00
• 6e0459c9bb
  Update SeqLengthToCsv_v1.0.py Godwin Ani 2024-01-15 14:59:32 -05:00
• 188839b99e
  Update SeqLengthToCsv_v1.0.py Godwin Ani 2024-01-15 14:59:17 -05:00
• 74986dc0c0
  Rename SeqLengthToCsv_Feb9.py to SeqLengthToCsv_v1.0.py Godwin Ani 2024-01-15 14:58:54 -05:00
• 895e2aaafe
  Update GC_identifier_v1.0.py Godwin Ani 2024-01-15 14:57:45 -05:00
• d415cca1e8
  Rename OG6_A_G.py to GC_identifier_v1.0.py Godwin Ani 2024-01-15 14:57:10 -05:00
• 88da115935
  Rename ClusterMC_Feb9.py to Cluster_v2.0.py Godwin Ani 2024-01-15 14:55:27 -05:00
• 0aced94675
  Update Assess_transcriptomes_v2.0.py Godwin Ani 2024-01-15 14:54:55 -05:00
• e756e8733b
  Update and rename gappiness.py to Gappiness_v2.0.py Godwin Ani 2024-01-15 14:54:18 -05:00
• 12ba81abb7
  Rename Assess_transcriptomes.py to Assess_transcriptomes_v2.0.py Godwin Ani 2024-01-15 14:53:03 -05:00
• 06a7bd81ef
  Rename plot_transcriptomes_v2.0.R to Plot_transcriptomes_v2.0.R Godwin Ani 2024-01-15 14:52:47 -05:00
• 297d0920fd
  Rename plot_transcriptomes.R to plot_transcriptomes_v2.0.R Godwin Ani 2024-01-15 14:52:31 -05:00
• cac7dbdc93
  Rename plot_assemblies.R to plot_transcriptomes.R Godwin Ani 2024-01-15 14:52:00 -05:00
• 36153e21c4
  Rename assess_transcriptomes.py to Assess_transcriptomes.py Godwin Ani 2024-01-15 14:51:21 -05:00
• ccb70d9b46
  More flexible OG identifier handling in preguidance.py Auden Cote-L'Heureux 2024-01-12 13:25:53 -05:00
• 9f2d34e056
  Add OG identifier default utils.py Auden Cote-L'Heureux 2024-01-12 13:25:17 -05:00
• d86742bf39
  Update headers Godwin Ani 2024-01-12 12:11:02 -05:00
• 06d63c6334
  Update headers Godwin Ani 2024-01-12 11:26:34 -05:00
• d90385ae27
  Update headers Godwin Ani 2024-01-12 11:26:02 -05:00
• d55b87f1d9
  Update headers Godwin Ani 2024-01-12 11:19:16 -05:00
• 316f7620ed
  Update headers Godwin Ani 2024-01-12 11:13:28 -05:00
• b37abda8d5
  Update headers Godwin Ani 2024-01-12 11:07:31 -05:00
• 05d15104cf
  Update headers Godwin Ani 2024-01-12 10:59:47 -05:00
• 085d9849e3
  Update headers Godwin Ani 2024-01-12 10:10:45 -05:00
• 8f47f87460
  Update headers Godwin Ani 2024-01-12 10:07:42 -05:00
• ba316d02ed
  Update headers Godwin Ani 2024-01-12 10:06:18 -05:00
• 6d1dd274ae
  Update headers Godwin Ani 2024-01-12 10:01:31 -05:00
• a7acdd26be
  Update headers Godwin Ani 2024-01-12 09:54:54 -05:00
• 39a3ecb5d8
  Changing default tip label font size Auden Cote-L'Heureux 2023-12-22 12:00:21 -05:00
• a53c89fdd7
  Updating headers in CladeSizes_v3.0.py Auden Cote-L'Heureux 2023-12-19 13:50:17 -05:00
• d4aed039fd
  Adding updated CladeSizes script with summary function Auden Cote-L'Heureux 2023-12-19 13:49:49 -05:00
• 2688df4a98
  Delete Utilities/for_trees/CladeSizes_v2.0.py Auden Cote-L'Heureux 2023-12-19 13:49:13 -05:00
• c655354a42
  Update and rename faralog.py to gappiness.py Auden Cote-L'Heureux 2023-12-19 13:28:40 -05:00
• 25b41672b3
  Updating default colors in ColorByClade_v2.1.py Auden Cote-L'Heureux 2023-12-18 11:21:49 -05:00
• 110e3b7479
  Fixing minor error in clade sizes script Auden Cote-L'Heureux 2023-12-06 20:11:53 -05:00
• 0cd6d05960
  Temporarily removing contamination loop Auden Cote-L'Heureux 2023-12-04 16:04:46 -05:00
• 333585acde
  added sim taxa and Og identifier flag Godwin Ani 2023-12-04 15:52:10 -05:00
• 304cebc73f
  Utils script with sim taxa and OG identifier flag Godwin Ani 2023-12-04 15:00:10 -05:00
• b466a30a96
  Updated preguidance with no logger dependency Godwin Ani 2023-12-04 14:54:57 -05:00
• a15ba2402d
  Setting -T AUTO in IQ-Tree Auden Cote-L'Heureux 2023-12-04 14:31:45 -05:00
• 8dfd0710ef
  TEMPORARILY putting the logger here Auden Cote-L'Heureux 2023-12-04 14:04:05 -05:00
• 9cf716d431
  Added clade-size (()()()) script Auden Cote-L'Heureux 2023-12-01 12:15:21 -05:00
• e9a28b4eaa
  Delete PTL2/Scripts/logger.py Auden Cote-L'Heureux 2023-11-27 15:46:55 -05:00
• 31fa46a149
  Rename seqs by gc3 width Godwin Ani 2023-11-27 15:42:16 -05:00
• f38496cbb1
  Update preguidance - OG6 and sim filter Godwin Ani 2023-11-27 15:16:21 -05:00
• 9f29a86863
  OG6/A/G, Sim Filter by taxa, Removed_seqs_file Godwin Ani 2023-11-27 15:15:58 -05:00
• 22bd67d2fa
  OG6/G/A, Sim_filter by taxa, and Sim_removed_seqs Godwin Ani 2023-11-27 15:15:50 -05:00
• bacb094028
  Cleaning up length filter Auden Cote-L'Heureux 2023-11-27 14:11:07 -05:00
• 0faa9f0b14
  Fixing stop codon 1/3 length issue Auden Cote-L'Heureux 2023-11-27 14:09:53 -05:00
• 4e1ceae627
  Delete Utilities/for_trees/ColorByClade_v2.0.py Auden Cote-L'Heureux 2023-11-27 13:54:09 -05:00
• 3dd53c1eb9
  Fixing rooting & ladderizing & node labels Auden Cote-L'Heureux 2023-11-27 13:53:02 -05:00
• 8872d1724d
  Update preguidance.py Auden Cote-L'Heureux 2023-11-24 12:35:21 -05:00
• 8fa40adf9c
  Adding version of contamination loop before November mods Auden Cote-L'Heureux 2023-11-22 11:41:05 -05:00
• e082b6bf3a
  Rename rename_tip_labels .py to rename_tip_labels.py MCLeleu 2023-11-15 16:41:31 +01:00
• f292cf3cf9
  Add files via upload Godwin Ani 2023-11-13 16:25:52 -05:00
• 1b587bf266
  Version of scripts used to successfully run conserved OGs on 11/13/23 Auden Cote-L'Heureux 2023-11-13 12:09:57 -05:00
• 842b229833
  Rename 6_SummaryStats.py to 5b_SummaryStats.py Auden Cote-L'Heureux 2023-11-10 10:21:35 -05:00
• 06e13e7caa
  Rename 5_FinalizeName.py to 5a_FinalizeName.py Auden Cote-L'Heureux 2023-11-10 10:21:24 -05:00
• c300980148
  f/paralogs assessment script Godwin Ani 2023-11-07 11:44:36 -05:00
• b8436d03dd
  For adding metadata to tree tip labels Godwin Ani 2023-11-06 10:15:53 -05:00
• 43a7439a02
  Adjusting sim filter, adding score to guidance removed seqs output Auden Cote-L'Heureux 2023-11-03 11:05:46 -04:00
• 72660b742b
  Adding CheckSetup.py to the Genomes Auden Cote-L'Heureux 2023-10-30 17:18:56 -04:00
• fbac4f6b09
  Add files via upload Auden Cote-L'Heureux 2023-10-30 16:40:40 -04:00
• b8ac13a0f0
  Delete PTL1/Transcriptomes/Scripts/__pycache__ directory Auden Cote-L'Heureux 2023-10-30 15:18:42 -04:00
• e90e177276
  Fixing small oversight in concatenate.py Auden Cote-L'Heureux 2023-10-30 13:00:07 -04:00
• 6f1c37bcbc
  Updating utils.py to account for addition of concatenation Auden Cote-L'Heureux 2023-10-30 12:49:43 -04:00
• 2868b53dfc
  Adding concatenation script Auden Cote-L'Heureux 2023-10-30 12:49:12 -04:00
• 4c4997ecff
  Update CountTaxonOccurence.py Auden Cote-L'Heureux 2023-10-24 11:20:52 -04:00
• b3fcdc7c3c
  Update CountTaxonOccurence.py Auden Cote-L'Heureux 2023-10-24 11:20:11 -04:00
• 81f54d2e1c
  Update and rename CountTreeTips.py to CountTaxonOccurence.py Auden Cote-L'Heureux 2023-10-24 11:19:50 -04:00
• 9edbf3b87c
  Small fix CountTreeTips.py Auden Cote-L'Heureux 2023-10-24 11:16:11 -04:00
• 8ae3f7ca57
  Rename count_tips.py to CountTreeTips.py Auden Cote-L'Heureux 2023-10-24 11:15:49 -04:00
• 9d07bca28c
  Updating arg parsing in tip counting script Auden Cote-L'Heureux 2023-10-24 11:15:37 -04:00
• 2280edaf5a
  Fixed variable reference error in preguidance.py Auden Cote-L'Heureux 2023-10-21 20:09:27 -04:00
• 156e4ee8d0
  Removed overlap/dissimilarity filter Auden Cote-L'Heureux 2023-10-19 12:49:35 -04:00
• f5140c487b
  Delete PTL2/Scripts/preguidance.py Auden Cote-L'Heureux 2023-10-19 12:48:40 -04:00
• 7169e3666a
  Added OF log to preguidance Auden Cote-L'Heureux 2023-10-15 17:37:43 -04:00
• 356fc287f0
  Delete PTL2/Scripts/preguidance.py Auden Cote-L'Heureux 2023-10-15 17:37:31 -04:00
• 7a438d250a
  Small print change in preguidance.py Auden Cote-L'Heureux 2023-10-15 17:25:58 -04:00
• 7b3860a449
  Update utils.py Auden Cote-L'Heureux 2023-10-13 10:09:16 -04:00
• f1d573458b
  Preventing same contig/OG number bug in 4_CountOGsDiamond.py Auden Cote-L'Heureux 2023-10-06 10:42:21 -04:00
• a515a08c61
  Fixing same contig/OG number bug in 6_FilterPartials.py Auden Cote-L'Heureux 2023-10-06 10:41:29 -04:00
• 694ece4648
  Typo Auden Cote-L'Heureux 2023-10-02 12:03:27 -04:00
• f4faf95555
  Delete PTL1/Transcriptomes/Scripts/8_SummaryStats.py Auden Cote-L'Heureux 2023-10-02 11:49:27 -04:00
• adc96d1dbc
  Delete PTL1/Transcriptomes/Scripts/7_FinalizeName.py Auden Cote-L'Heureux 2023-10-02 11:49:20 -04:00
• 1ee6f5ceb6
  Small changes, see description Auden Cote-L'Heureux 2023-10-02 11:49:03 -04:00
• b2e381e01d
  Typo fix Auden Cote-L'Heureux 2023-10-02 11:12:44 -04:00
• 4b934b8de2
  Rename 4_InFrameStopCodonEsimator.py to 4_InFrameStopCodonEstimator.py Auden Cote-L'Heureux 2023-10-02 11:11:49 -04:00
• fa294909c5
  Updates to script 6 filters & script names Auden Cote-L'Heureux 2023-09-29 13:20:49 -04:00
• f9d747ce38
  Delete PTL1/Transcriptomes/Scripts/7_FinalizeName.py Auden Cote-L'Heureux 2023-09-29 13:20:17 -04:00
• 5f28d4447f
  Delete PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py Auden Cote-L'Heureux 2023-09-29 13:20:11 -04:00
• eb3db88688
  Delete PTL1/Transcriptomes/Scripts/6_FilterPartials.py Auden Cote-L'Heureux 2023-09-29 13:20:05 -04:00
• 02ec29d737
  Delete PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py Auden Cote-L'Heureux 2023-09-29 13:19:55 -04:00
• 0b6823d007
  Delete PTL1/Transcriptomes/Scripts/4_InFrameStopFreq.py Auden Cote-L'Heureux 2023-09-29 13:19:49 -04:00
• 6746899daa
  Delete PTL1/Transcriptomes/Scripts/3_CountOGsDiamond.py Auden Cote-L'Heureux 2023-09-29 13:19:43 -04:00