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Author	SHA1	Message	Date
Auden Cote-L'Heureux	1d7749b3a6	Updating header in 1a_TranscriptLengthFilter.py	2025-01-19 10:57:44 -05:00
Auden Cote-L'Heureux	375bfef45e	Updating header wrapper.py	2025-01-19 10:55:37 -05:00
Auden Cote-L'Heureux	f5bb221378	Updating header in CheckSetup.py	2025-01-19 10:54:49 -05:00
Katzlab	31d0a8ddb2	Update CUB.py ... headers	2025-01-19 10:54:01 -05:00
Katzlab	3491166695	Update 5b_SummaryStats.py ... updated headers	2025-01-19 10:51:39 -05:00
Katzlab	cd226beb9c	Update 4_CountOGsDiamond.py	2025-01-19 10:49:41 -05:00
Auden Cote-L'Heureux	10a8c2f78a	Notes in run_eukphylo.sh, further updates needed	2025-01-19 10:27:34 -05:00
Auden Cote-L'Heureux	2173eda5a0	Update run_eukphylo.sh	2025-01-17 10:34:37 -05:00
Auden Cote-L'Heureux	60b0f9a9b4	Update contamination.py	2025-01-17 10:16:55 -05:00
Auden Cote-L'Heureux	bd72ed3a43	Update and rename phylotol.py to eukphylo.py	2025-01-17 10:16:27 -05:00
Auden Cote-L'Heureux	0fbd2ae863	Rename run_phylotol.sh to run_eukphylo.sh	2025-01-17 10:16:01 -05:00
Auden Cote-L'Heureux	19943a13fd	Delete PTL1_gene_families	2025-01-17 10:03:53 -05:00
Auden Cote-L'Heureux	04fe7029d2	Changing to use EukPhylo	2025-01-17 09:50:54 -05:00
Adri K. Grow	fe7ef7b71a	Update and rename ProcessAndRenamePlateTranscripts_AKG.py to ProcessAndRenamePlateTranscripts.py	2025-01-15 11:25:16 -05:00
Adri K. Grow	2ad02897c8	Add files via upload	2025-01-15 11:22:39 -05:00
Auden Cote-L'Heureux	eb9e81f4c0	adding iqtree-fast	2025-01-12 12:35:53 -05:00
Auden Cote-L'Heureux	4f5bce5963	Update utils.py	2025-01-12 12:35:05 -05:00
Auden Cote-L'Heureux	d595a51b4f	adding 'allow_large_files' flag	2025-01-09 12:20:59 -05:00
Auden Cote-L'Heureux	31a9295485	Adding flag for large files to guidance.py	2025-01-09 12:19:51 -05:00
Auden Cote-L'Heureux	733851b957	Adding trimal cutoff as parameter	2025-01-09 12:11:54 -05:00
Auden Cote-L'Heureux	c0dfdb6248	Adding trimal cutoff as parameter	2025-01-09 12:11:10 -05:00
Auden Cote-L'Heureux	baf5fd037d	Adding TrimAl cutoff as parameter	2025-01-09 12:09:36 -05:00
Auden Cote-L'Heureux	1e543b3989	Adding TPM calculating script (Salmon)	2025-01-09 12:06:10 -05:00
Auden Cote-L'Heureux	a8a2a5ff2d	Moving CountTaxonOccurence.py	2025-01-08 10:38:23 -05:00
Adri K. Grow	1c309f8e10	Update ReadMapping.py	2024-12-06 12:20:50 -05:00
Adri K. Grow	61f808343f	Update run_phylotol.sh	2024-11-26 13:04:53 -05:00
Godwin Ani	22eb559650	Update run_phylotol.sh	2024-11-12 09:01:44 -05:00
Adri K. Grow	dcf4079b86	Update wrapper_submit.sh ... Updated modules for current grid use.	2024-11-11 21:19:16 -05:00
Godwin Ani	f2701e7f65	Update run_phylotol.sh	2024-11-11 17:01:32 -05:00
Adri K. Grow	a0b45ed2c8	Update CladeSizes.py ... Modified to work with clade grabbed input file names.	2024-11-11 08:59:47 -05:00
Auden Cote-L'Heureux	fb6e7aa6e7	Changing CladeGrabbing.py to use less than or equal to for number of contaminants	2024-11-01 10:34:57 -04:00
Auden Cote-L'Heureux	d249add545	Add files via upload	2024-10-17 16:45:55 -04:00
MCLeleu	d57fdad826	Delete Am_tu_He24_assembledTranscripts.fasta	2024-10-15 11:46:54 -04:00
MCLeleu	f18717ac6b	Add files via upload	2024-10-15 11:46:37 -04:00
MCLeleu	da6ac878d3	Add files via upload	2024-10-15 11:46:12 -04:00
MCLeleu	eb81b5ebfa	Delete PTL1/Transcriptomes/TestData/Sr_rh_Amon_assembledTranscripts.fasta	2024-10-15 11:45:51 -04:00
MCLeleu	679f1a10c8	Delete PTL1/Transcriptomes/TestData/Sr_rh_Aa01_assembledTranscripts.fasta	2024-10-15 11:45:32 -04:00
MCLeleu	85be0f31ca	Delete PTL1/Transcriptomes/TestData/Sr_rh_Emac_assembledTranscripts.fasta	2024-10-15 11:45:21 -04:00
MCLeleu	4472f44e36	Add files via upload	2024-10-15 11:43:54 -04:00
MCLeleu	e862010cfc	Add files via upload	2024-10-15 11:43:13 -04:00
Katzlab	d7f02a243c	Fixing concat_target_taxa file read error in concatenation	2024-08-26 15:56:42 -04:00
Katzlab	4b8a3fbe64	Delete PTL2/Scripts/utils.py	2024-08-26 15:56:15 -04:00
Katzlab	c4aab9eaef	Delete PTL2/Scripts/concatenate.py	2024-08-26 15:56:09 -04:00
Katzlab	7904ec8b35	Fixing concat taxon list read error	2024-08-22 11:59:58 -04:00
Katzlab	41cc1354b3	Fixing taxon list read error in concatenate.py	2024-08-22 11:59:38 -04:00
Katzlab	4676ef2b53	Delete Utilities/README.md v6.0	2024-08-14 11:59:56 -04:00
Katzlab	2a305403a5	Update README.md	2024-08-14 11:58:41 -04:00
Katzlab	9ecc2d899a	Delete HookDB directory	2024-08-14 11:52:58 -04:00
MCLeleu	4dc9a3fe74	Delete PTL2/Examplar_runs/Running_PTLp2/Output directory	2024-08-14 10:58:17 -04:00
MCLeleu	246900721c	Delete PTL2/Examplar_runs/Running_PTLp2/Input directory	2024-08-14 10:58:01 -04:00