From 04a1c76a2d01c2e0fef2048865852725cbd9e5bb Mon Sep 17 00:00:00 2001 From: "Godwin N. Ani" Date: Mon, 7 Apr 2025 15:06:34 -0400 Subject: [PATCH] Updated EukPhylo QuickStart (markdown) --- EukPhylo-QuickStart.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EukPhylo-QuickStart.md b/EukPhylo-QuickStart.md index 42e008c..9727cfe 100644 --- a/EukPhylo-QuickStart.md +++ b/EukPhylo-QuickStart.md @@ -223,7 +223,7 @@ Options: |`--subsister_rules`|only in subsisters mode|Valid path|Path to a text file containing subsisters rules|NA| |`--clade_grabbing_rules`|only in clade mode|Valid path|Path to a text file containing clade-grabbing rules|NA| |`--clade_grabbing_exceptions`|no|Valid path|List of taxa to _not_ remove for any reason|NA| -|`--cl_tree_method`|no|`iqtree`, `raxml`, `fasttree`, `iqtree_fast`|Tree-building method to use in each contamination loop iteration|`fasttree`| +|`--cl_tree_method`|no|`iqtree`, `raxml`, `fasttree`, `iqtree_fast`|Tree-building method to use in each contamination loop iteration|`iqtree_fast`| |`--cl_alignment_method`|no|`mafft_only`, `guidance`|Alignment method to use in each contamination loop iteration|`mafft_only`| |`--cl_exclude_taxa`|no|Valid path|Path to a file containing taxon names present in input MSA/tree files but which should be removed in the first iteration of the contamination loop|NA|