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Author	SHA1	Message	Date
Godwin Ani	cac7dbdc93	Rename plot_assemblies.R to plot_transcriptomes.R	2024-01-15 14:52:00 -05:00
Godwin Ani	36153e21c4	Rename assess_transcriptomes.py to Assess_transcriptomes.py	2024-01-15 14:51:21 -05:00
Auden Cote-L'Heureux	ccb70d9b46	More flexible OG identifier handling in preguidance.py	2024-01-12 13:25:53 -05:00
Auden Cote-L'Heureux	9f2d34e056	Add OG identifier default utils.py	2024-01-12 13:25:17 -05:00
Godwin Ani	d86742bf39	Update headers	2024-01-12 12:11:02 -05:00
Godwin Ani	06d63c6334	Update headers	2024-01-12 11:26:34 -05:00
Godwin Ani	d90385ae27	Update headers	2024-01-12 11:26:02 -05:00
Godwin Ani	d55b87f1d9	Update headers	2024-01-12 11:19:16 -05:00
Godwin Ani	316f7620ed	Update headers	2024-01-12 11:13:28 -05:00
Godwin Ani	b37abda8d5	Update headers	2024-01-12 11:07:31 -05:00
Godwin Ani	05d15104cf	Update headers	2024-01-12 10:59:47 -05:00
Godwin Ani	085d9849e3	Update headers	2024-01-12 10:10:45 -05:00
Godwin Ani	8f47f87460	Update headers	2024-01-12 10:07:42 -05:00
Godwin Ani	ba316d02ed	Update headers	2024-01-12 10:06:18 -05:00
Godwin Ani	6d1dd274ae	Update headers	2024-01-12 10:01:31 -05:00
Godwin Ani	a7acdd26be	Update headers	2024-01-12 09:54:54 -05:00
Auden Cote-L'Heureux	39a3ecb5d8	Changing default tip label font size	2023-12-22 12:00:21 -05:00
Auden Cote-L'Heureux	a53c89fdd7	Updating headers in CladeSizes_v3.0.py	2023-12-19 13:50:17 -05:00
Auden Cote-L'Heureux	d4aed039fd	Adding updated CladeSizes script with summary function	2023-12-19 13:49:49 -05:00
Auden Cote-L'Heureux	2688df4a98	Delete Utilities/for_trees/CladeSizes_v2.0.py	2023-12-19 13:49:13 -05:00
Auden Cote-L'Heureux	c655354a42	Update and rename faralog.py to gappiness.py	2023-12-19 13:28:40 -05:00
Auden Cote-L'Heureux	25b41672b3	Updating default colors in ColorByClade_v2.1.py	2023-12-18 11:21:49 -05:00
Auden Cote-L'Heureux	110e3b7479	Fixing minor error in clade sizes script	2023-12-06 20:11:53 -05:00
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