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Author	SHA1	Message	Date
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
Auden Cote-L'Heureux	1ee6f5ceb6	Small changes, see description ... - Default partial filter cov threshold is 20% - Changed script names - Made requirement of conspecific names file explicit when using XPC	2023-10-02 11:49:03 -04:00
Auden Cote-L'Heureux	b2e381e01d	Typo fix	2023-10-02 11:12:44 -04:00
Auden Cote-L'Heureux	4b934b8de2	Rename 4_InFrameStopCodonEsimator.py to 4_InFrameStopCodonEstimator.py	2023-10-02 11:11:49 -04:00
Auden Cote-L'Heureux	fa294909c5	Updates to script 6 filters & script names	2023-09-29 13:20:49 -04:00
Auden Cote-L'Heureux	f9d747ce38	Delete PTL1/Transcriptomes/Scripts/7_FinalizeName.py	2023-09-29 13:20:17 -04:00
Auden Cote-L'Heureux	5f28d4447f	Delete PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py	2023-09-29 13:20:11 -04:00
Auden Cote-L'Heureux	eb3db88688	Delete PTL1/Transcriptomes/Scripts/6_FilterPartials.py	2023-09-29 13:20:05 -04:00
Auden Cote-L'Heureux	02ec29d737	Delete PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py	2023-09-29 13:19:55 -04:00
Auden Cote-L'Heureux	0b6823d007	Delete PTL1/Transcriptomes/Scripts/4_InFrameStopFreq.py	2023-09-29 13:19:49 -04:00
Auden Cote-L'Heureux	6746899daa	Delete PTL1/Transcriptomes/Scripts/3_CountOGsDiamond.py	2023-09-29 13:19:43 -04:00
Auden Cote-L'Heureux	18981a792f	Delete PTL1/Transcriptomes/Scripts/2b_remove_Bact.py	2023-09-29 13:19:36 -04:00
Auden Cote-L'Heureux	b6f439e7d6	Delete PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py	2023-09-29 13:19:30 -04:00
Auden Cote-L'Heureux	3e01100304	Delete PTL1/Transcriptomes/Scripts/1b_XSpeciesContaminationAgnes.py	2023-09-29 13:19:23 -04:00
Auden Cote-L'Heureux	67bbdd30b8	Delete PTL1/Transcriptomes/Scripts/1a_ContigFiltStats.py	2023-09-29 13:19:12 -04:00
Adri K. Grow	6a0b0ace3a	Add files via upload	2023-09-26 12:49:36 -04:00
Auden Cote-L'Heureux	032233968d	Reverting to version of trees.py from before contamination loop work	2023-09-18 12:58:48 -04:00
Auden Cote-L'Heureux	fe813b678d	Delete PTL2/Scripts/trees.py	2023-09-18 12:58:25 -04:00
Auden Cote-L'Heureux	7d54bb7416	New script 6 with revised length filtration	2023-09-18 10:06:36 -04:00
Auden Cote-L'Heureux	8ccb6eb9a7	Delete PTL1/Transcriptomes/Scripts/6_FilterPartials.py	2023-09-18 10:05:39 -04:00
Auden Cote-L'Heureux	106b2e2d89	Added annotation to 4_CountOGsDiamond.py	2023-09-18 10:04:25 -04:00
Auden Cote-L'Heureux	8e561dc735	New Script 6 with fixed ciliate genetic code issue	2023-09-18 10:02:48 -04:00
Auden Cote-L'Heureux	d300ade1b0	Delete PTL1/Genomes/Scripts/6_SummaryStats.py	2023-09-18 10:02:35 -04:00
Auden Cote-L'Heureux	3015aaa2eb	New Script 4 with added Hook-relative length filter	2023-09-18 10:02:06 -04:00
Auden Cote-L'Heureux	a45f921955	Delete PTL1/Genomes/Scripts/4_CountOGsDiamond.py	2023-09-18 10:01:44 -04:00
Auden Cote-L'Heureux	bceb9ff1de	Delete PTL1/Genomes/Output directory	2023-09-13 14:17:43 -04:00
Auden Cote-L'Heureux	8a2010d510	Delete PTL1/Transcriptomes/Output directory	2023-09-13 14:17:32 -04:00
Adri K. Grow	e502d2638f	Add files via upload	2023-09-01 14:35:08 -04:00
Godwin Ani	a7832842ae	Fixed Tree script by Auden ... Accepts both .fas and .fasta files now.	2023-08-31 13:05:16 -04:00
Godwin Ani	7af603d7f4	Delete PTL2/Scripts/trees.py ... Script with .fas and .fasta issue.	2023-08-31 13:04:18 -04:00
Adri K. Grow	c1b955d9b2	Add files via upload	2023-08-30 09:32:26 -04:00
Adri K. Grow	5d98dea9ff	Delete run_phylotol.sh	2023-08-30 09:31:58 -04:00
Adri K. Grow	c1d8ea93fc	Add files via upload	2023-08-30 09:29:33 -04:00