From 7a2320284a0408ae6daff765054b1c6c2af3c787 Mon Sep 17 00:00:00 2001 From: "Godwin N. Ani" Date: Thu, 17 Jul 2025 14:46:52 -0400 Subject: [PATCH] Update utils.py --- PTL2/Scripts/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PTL2/Scripts/utils.py b/PTL2/Scripts/utils.py index 8f90971..8f9dc56 100644 --- a/PTL2/Scripts/utils.py +++ b/PTL2/Scripts/utils.py @@ -44,7 +44,7 @@ def get_params(): core.add_argument('--col_cutoff', default = 0.0, type = float, help = 'During guidance, columns are removed if their score is below this cutoff') core.add_argument('--res_cutoff', default = 0.0, type = float, help = 'During guidance, residues are removed if their score is below this cutoff') core.add_argument('--guidance_threads', default = 20, type = int, help = 'Number of threads to allocate to Guidance') - core.add_argument('--trimal_cutoff', default = 0.05, type = float, help = 'Gap masking threshold for TrimAl. The maximum proportion of sequences without gaps for a site to be removed (i.e. to remove sites with 95% or more gaps, set this parameter to 0.05).') + core.add_argument('--trimal_cutoff', default = 0.3, type = float, help = 'Gap masking threshold for TrimAl. The maximum proportion of sequences without gaps for a site to be removed (i.e. to remove sites with 70% or more gaps, set this parameter to 0.3).') core.add_argument('--allow_large_files', action = 'store_true', help = 'Allow files with more than 2,000 sequences to run through Guidance.') CL = parser.add_argument_group('Contamination loop parameters')