YuuMJ1997/EukPhylo
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340 Commits

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Author SHA1 Message Date
Auden Cote-L'Heureux
0cd6d05960
Temporarily removing contamination loop 2023-12-04 16:04:46 -05:00
Godwin Ani
333585acde
added sim taxa and Og identifier flag 2023-12-04 15:52:10 -05:00
Godwin Ani
304cebc73f
Utils script with sim taxa and OG identifier flag 2023-12-04 15:00:10 -05:00
Godwin Ani
b466a30a96
Updated preguidance with no logger dependency 2023-12-04 14:54:57 -05:00
Auden Cote-L'Heureux
a15ba2402d
Setting -T AUTO in IQ-Tree 2023-12-04 14:31:45 -05:00
Auden Cote-L'Heureux
8dfd0710ef
TEMPORARILY putting the logger here 2023-12-04 14:04:05 -05:00
Auden Cote-L'Heureux
9cf716d431
Added clade-size (()()()) script 2023-12-01 12:15:21 -05:00
Auden Cote-L'Heureux
e9a28b4eaa
Delete PTL2/Scripts/logger.py 2023-11-27 15:46:55 -05:00
Godwin Ani
31fa46a149
Rename seqs by gc3 width 2023-11-27 15:42:16 -05:00
Godwin Ani
f38496cbb1
Update preguidance - OG6 and sim filter 2023-11-27 15:16:21 -05:00
Godwin Ani
9f29a86863
OG6/A/G, Sim Filter by taxa, Removed_seqs_file 2023-11-27 15:15:58 -05:00
Godwin Ani
22bd67d2fa
OG6/G/A, Sim_filter by taxa, and Sim_removed_seqs 2023-11-27 15:15:50 -05:00
Auden Cote-L'Heureux
bacb094028
Cleaning up length filter 2023-11-27 14:11:07 -05:00
Auden Cote-L'Heureux
0faa9f0b14
Fixing stop codon 1/3 length issue 2023-11-27 14:09:53 -05:00
Auden Cote-L'Heureux
4e1ceae627
Delete Utilities/for_trees/ColorByClade_v2.0.py 2023-11-27 13:54:09 -05:00
Auden Cote-L'Heureux
3dd53c1eb9
Fixing rooting & ladderizing & node labels 2023-11-27 13:53:02 -05:00
Auden Cote-L'Heureux
8872d1724d
Update preguidance.py 2023-11-24 12:35:21 -05:00
Auden Cote-L'Heureux
8fa40adf9c
Adding version of contamination loop before November mods 2023-11-22 11:41:05 -05:00
MCLeleu
e082b6bf3a
Rename rename_tip_labels .py to rename_tip_labels.py 
Removed a space in the filename
 2023-11-15 16:41:31 +01:00
Godwin Ani
f292cf3cf9
Add files via upload 2023-11-13 16:25:52 -05:00
Auden Cote-L'Heureux
1b587bf266
Version of scripts used to successfully run conserved OGs on 11/13/23 
Recent updates:
Similarity filter adjusted to have on/off parameter
Blacklist implemented & tested
Output list of Guidance-removed sequences with seq scores
Temp/intermediate file naming issue fixed
 2023-11-13 12:09:57 -05:00
Auden Cote-L'Heureux
842b229833
Rename 6_SummaryStats.py to 5b_SummaryStats.py 2023-11-10 10:21:35 -05:00
Auden Cote-L'Heureux
06e13e7caa
Rename 5_FinalizeName.py to 5a_FinalizeName.py 2023-11-10 10:21:24 -05:00
Godwin Ani
c300980148
f/paralogs assessment script 2023-11-07 11:44:36 -05:00
Godwin Ani
b8436d03dd
For adding metadata to tree tip labels 2023-11-06 10:15:53 -05:00
Auden Cote-L'Heureux
43a7439a02
Adjusting sim filter, adding score to guidance removed seqs output 2023-11-03 11:05:46 -04:00
Auden Cote-L'Heureux
72660b742b
Adding CheckSetup.py to the Genomes 2023-10-30 17:18:56 -04:00
Auden Cote-L'Heureux
fbac4f6b09
Add files via upload 2023-10-30 16:40:40 -04:00
Auden Cote-L'Heureux
b8ac13a0f0
Delete PTL1/Transcriptomes/Scripts/__pycache__ directory 2023-10-30 15:18:42 -04:00
Auden Cote-L'Heureux
e90e177276
Fixing small oversight in concatenate.py 2023-10-30 13:00:07 -04:00
Auden Cote-L'Heureux
6f1c37bcbc
Updating utils.py to account for addition of concatenation 2023-10-30 12:49:43 -04:00
Auden Cote-L'Heureux
2868b53dfc
Adding concatenation script 2023-10-30 12:49:12 -04:00
Auden Cote-L'Heureux
4c4997ecff
Update CountTaxonOccurence.py 2023-10-24 11:20:52 -04:00
Auden Cote-L'Heureux
b3fcdc7c3c
Update CountTaxonOccurence.py 2023-10-24 11:20:11 -04:00
Auden Cote-L'Heureux
81f54d2e1c
Update and rename CountTreeTips.py to CountTaxonOccurence.py 2023-10-24 11:19:50 -04:00
Auden Cote-L'Heureux
9edbf3b87c
Small fix CountTreeTips.py 2023-10-24 11:16:11 -04:00
Auden Cote-L'Heureux
8ae3f7ca57
Rename count_tips.py to CountTreeTips.py 2023-10-24 11:15:49 -04:00
Auden Cote-L'Heureux
9d07bca28c
Updating arg parsing in tip counting script 2023-10-24 11:15:37 -04:00
Auden Cote-L'Heureux
2280edaf5a
Fixed variable reference error in preguidance.py 2023-10-21 20:09:27 -04:00
Auden Cote-L'Heureux
156e4ee8d0
Removed overlap/dissimilarity filter 
(Deleted previous version because of technical GitHub issues)
 2023-10-19 12:49:35 -04:00
Auden Cote-L'Heureux
f5140c487b
Delete PTL2/Scripts/preguidance.py 2023-10-19 12:48:40 -04:00
Auden Cote-L'Heureux
7169e3666a
Added OF log to preguidance 2023-10-15 17:37:43 -04:00
Auden Cote-L'Heureux
356fc287f0
Delete PTL2/Scripts/preguidance.py 2023-10-15 17:37:31 -04:00
Auden Cote-L'Heureux
7a438d250a
Small print change in preguidance.py 2023-10-15 17:25:58 -04:00
Auden Cote-L'Heureux
7b3860a449
Update utils.py 2023-10-13 10:09:16 -04:00
Auden Cote-L'Heureux
f1d573458b
Preventing same contig/OG number bug in 4_CountOGsDiamond.py 2023-10-06 10:42:21 -04:00
Auden Cote-L'Heureux
a515a08c61
Fixing same contig/OG number bug in 6_FilterPartials.py 2023-10-06 10:41:29 -04:00
Auden Cote-L'Heureux
694ece4648
Typo 2023-10-02 12:03:27 -04:00
Auden Cote-L'Heureux
f4faf95555
Delete PTL1/Transcriptomes/Scripts/8_SummaryStats.py 2023-10-02 11:49:27 -04:00
Auden Cote-L'Heureux
adc96d1dbc
Delete PTL1/Transcriptomes/Scripts/7_FinalizeName.py 2023-10-02 11:49:20 -04:00