90 Commits

Author	SHA1	Message	Date
Godwin Ani	f2701e7f65	Update run_phylotol.sh	2024-11-11 17:01:32 -05:00
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
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
MCLeleu	8ac84ad0f3	Create README.txt	2024-08-14 10:50:03 -04:00
MCLeleu	1cc10f71a6	Create README.txt	2024-08-14 10:49:17 -04:00
MCLeleu	aad1696e8d	Create test	2024-08-14 10:38:58 -04:00
MCLeleu	c090c7d0c1	Create test	2024-08-14 10:38:42 -04:00
MCLeleu	5703e9d78b	Add files via upload	2024-08-14 16:37:43 +02:00
MCLeleu	68ccdaaa25	Add files via upload	2024-08-14 16:36:38 +02:00
MCLeleu	dd51f21885	Create run_phylotol_command_line.txt	2024-08-14 10:36:09 -04:00
MCLeleu	c73c93e3b5	Create run_phylotol_command_line.txt	2024-08-14 10:35:19 -04:00
MCLeleu	c7afaf41ed	Add files via upload	2024-08-14 16:34:08 +02:00
MCLeleu	2b9a887c04	Create run_phylotol_command_line.txt ... Example command line to run PhyloToL	2024-08-14 10:33:21 -04:00
Katzlab	6061157249	Delete PTL2/README.md	2024-08-09 10:05:54 -04:00
Auden Cote-L'Heureux	426d51ea85	Changing default output location in utils.py	2024-05-29 12:44:15 -04:00
Auden Cote-L'Heureux	f4b29ca82d	Fixing _ vs dot yet again in trees.py	2024-05-16 19:27:06 -04:00
Adri K. Grow	d6b89c23d1	Update run_phylotol.sh	2024-05-15 10:27:00 -04:00
Auden Cote-L'Heureux	2ac482572d	Fixing dot vs dash in trees.py	2024-05-02 14:18:32 -04:00
MCLeleu	0eb002a1bd	Update trees.py ... Changed -T AUTO for -T 10 on the iqtree line	2024-04-17 15:08:24 -04:00
Auden Cote-L'Heureux	18f4686223	Fixing underscore/dot issue in trees.py	2024-04-15 16:25:32 -04:00
Godwin Ani	2f67243515	Add files via upload	2024-04-11 14:43:53 -04:00
Godwin Ani	21e54ab7e4	Reverting to previous version	2024-04-01 11:04:37 -04:00
Godwin Ani	13e6d300c5	Adding keep_iter parameter	2024-03-22 15:07:25 -04:00
Godwin Ani	80ad29e6d5	Adding keep_iter parameter	2024-03-22 15:05:54 -04:00
Adri K. Grow	87840891d6	Add files via upload	2024-03-09 11:06:45 -05:00
Adri K. Grow	ce0649bf14	Delete PTL2/run_phylotol.sh	2024-03-09 11:05:59 -05:00
Auden Cote-L'Heureux	75b06a788e	annotating concatenate.py	2024-02-07 12:52:47 -05:00
Auden Cote-L'Heureux	920b3b4ad4	annotating contamination.py	2024-02-07 12:48:38 -05:00
Auden Cote-L'Heureux	23b81f83f7	annotating trees.py	2024-02-07 12:30:22 -05:00
Auden Cote-L'Heureux	7220b81402	annotating guidance.py	2024-02-07 12:18:46 -05:00
Auden Cote-L'Heureux	80409a22ff	annotating preguidance.py	2024-02-07 12:04:30 -05:00
Auden Cote-L'Heureux	c00780e313	annotating phylotol.py	2024-02-07 11:52:42 -05:00
Auden Cote-L'Heureux	c308864f5c	annotating utils.py	2024-02-07 11:52:08 -05:00
Auden Cote-L'Heureux	b7a3d1ac12	annotating phylotol.py	2024-02-07 11:46:40 -05:00
Auden Cote-L'Heureux	0a7ab708b9	Updating contamination loop parameters in utils.py	2024-02-07 11:36:45 -05:00
Auden Cote-L'Heureux	877aabd2ef	adding contamination loop back to wrapper	2024-02-07 11:31:03 -05:00
Auden Cote-L'Heureux	0f2ae76d13	exiting after errors in guidance.py	2024-02-07 11:30:26 -05:00
Auden Cote-L'Heureux	b981641f62	removing calls to logger in trees.py	2024-02-07 11:29:55 -05:00
Auden Cote-L'Heureux	556b8646ba	removing calls to logger in guidance.py	2024-02-07 11:28:07 -05:00
Auden Cote-L'Heureux	604a4af182	Delete PTL2/Scripts/logger.py	2024-02-07 11:25:06 -05:00
Auden Cote-L'Heureux	fff0032c0d	num_contams to float for proportional running contamination.py	2024-02-07 11:24:54 -05:00
Auden Cote-L'Heureux	9844842aed	Add files via upload	2024-02-07 11:23:49 -05:00
Auden Cote-L'Heureux	59bf186e91	Small update to concatenate.py	2024-01-24 11:58:57 -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