84 Commits

Author	SHA1	Message	Date
Godwin N. Ani	4e52430af7	Update guidance.py	2025-03-25 12:35:43 -04:00
Godwin N. Ani	fdea233780	Update guidance.py	2025-03-25 12:16:02 -04:00
Godwin N. Ani	cf0948023d	Update guidance.py	2025-03-24 10:17:36 -04:00
Godwin N. Ani	04c41a6f44	Update guidance.py	2025-03-24 10:16:53 -04:00
Godwin N. Ani	c39df0e39d	Update utils.py	2025-03-24 10:11:35 -04:00
Adri K. Grow	030401e9b0	Update guidance.py	2025-02-14 13:57:57 -05:00
Auden Cote-L'Heureux	fc190415ee	Updating headers in utils.py	2025-01-19 11:09:21 -05:00
Auden Cote-L'Heureux	743d650b74	updating header in trees.py	2025-01-19 11:08:08 -05:00
Auden Cote-L'Heureux	676a11a287	updating header in preguidance.py	2025-01-19 11:07:49 -05:00
Auden Cote-L'Heureux	0df7470b92	updating header in guidance.py	2025-01-19 11:07:25 -05:00
Auden Cote-L'Heureux	3dc60dcd2e	updating header in concatenate.py	2025-01-19 11:06:23 -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	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
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
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
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
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