78 Commits

Author	SHA1	Message	Date
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
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	e9a28b4eaa	Delete PTL2/Scripts/logger.py	2023-11-27 15:46:55 -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	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
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	43a7439a02	Adjusting sim filter, adding score to guidance removed seqs output	2023-11-03 11:05:46 -04:00