145 Commits

Author	SHA1	Message	Date
Godwin N. Ani	343496b598	Delete PTL2/Black_and_Grey_list_GuidanceSisSubsisters_RemovedSeq_Conserved_PTLms_June2024_ML.txt	2025-07-17 11:40:56 -04:00
Godwin N. Ani	3f9ef410a7	Rename Black_and_Grey_list_GuidanceSisSubsisters_RemovedSeq_Conserved_PTLms_June2024_ML (1).txt to Black_and_Grey_list_GuidanceSisSubsisters_RemovedSeq_Conserved_PTLms_June2024_ML.txt	2025-07-17 11:31:34 -04:00
Godwin N. Ani	fb5353fe96	Blacklist_and_greylist	2025-07-17 11:31:09 -04:00
Godwin N. Ani	4e63a165b7	Update contamination.py	2025-07-09 13:59:38 -04:00
Godwin N. Ani	99647c87bc	Update contamination.py	2025-07-09 13:59:28 -04:00
Katzlab	ef6b633de7	Update guidance.py ... tidying comments	2025-06-18 08:43:19 -04:00
Katzlab	c891188eec	Update guidance.py ... updated comments only to clarify versions	2025-06-18 08:37:19 -04:00
Adri K. Grow	d32fbcc4e8	Update guidance.py ... Updated guidance command for local HPC users	2025-06-02 11:23:34 -04:00
GiuliaRibeiro	9e4d605bff	Update trees.py	2025-04-18 13:01:33 -04:00
Auden Cote-L'Heureux	d01086e017	Update headers	2025-04-18 09:09:24 -04:00
Auden Cote-L'Heureux	e0930c5748	Update header for new guidance version	2025-04-18 09:09:03 -04:00
Auden Cote-L'Heureux	16a96f137e	Update guidance_path param	2025-04-18 08:48:42 -04:00
Auden Cote-L'Heureux	fa1f50e6f0	Update guidance_path param	2025-04-18 08:45:40 -04:00
Auden Cote-L'Heureux	9239110401	Updating guidance_path param	2025-04-18 08:45:23 -04:00
Auden Cote-L'Heureux	dc813c351a	Update utils.py	2025-04-18 08:44:21 -04:00
Auden Cote-L'Heureux	e452ae0117	Making the --concat_target_taxa argument optional	2025-04-15 16:23:19 -04:00
Godwin N. Ani	2651fe7b89	Update utils.py	2025-04-07 14:56:38 -04:00
Godwin N. Ani	c92f490837	Update contamination.py	2025-04-07 12:36:17 -04:00
Godwin N. Ani	7074a1e71a	Update contamination.py	2025-04-07 12:24:56 -04:00
Godwin N. Ani	95b26b1880	Update contamination.py	2025-04-07 12:20:56 -04:00
Godwin N. Ani	fba84adb17	Update contamination.py	2025-04-07 11:54:36 -04:00
Godwin N. Ani	8c7a1a2eed	Update contamination.py	2025-04-07 11:29:15 -04:00
Godwin N. Ani	e8aa277e44	Update contamination.py	2025-04-07 11:20:34 -04:00
Godwin N. Ani	998ce5bd9c	Update contamination.py	2025-04-07 11:06:32 -04:00
Godwin N. Ani	0cfea8840c	Update contamination.py	2025-04-04 15:28:08 -04:00
Auden Cote-L'Heureux	d161957d86	Taking out 'both' option of contamination loop	2025-03-28 15:40:58 -04:00
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	d1b9a64e60	Update run_eukphylo.sh	2025-03-13 17:23:19 -04:00
Adri K. Grow	030401e9b0	Update guidance.py	2025-02-14 13:57:57 -05:00
Adri K. Grow	feab503fb6	Update run_eukphylo.sh	2025-02-13 18:16:29 -05:00
Adri K. Grow	d4f27a3032	Update run_eukphylo.sh	2025-02-13 18:01:48 -05:00
Auden Cote-L'Heureux	a559f61567	Generalizing and adding examples to run_eukphylo.sh	2025-01-22 12:28:04 -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	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	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