110 Commits

Author	SHA1	Message	Date
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
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
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
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