From 9cf5952485f606ae9c0c2d663875837ce7450cf0 Mon Sep 17 00:00:00 2001 From: "Godwin N. Ani" Date: Mon, 7 Apr 2025 15:05:22 -0400 Subject: [PATCH] Updated EukPhylo Part 2: MSAs, trees, and contamination loop (markdown) --- EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md b/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md index db8ede6..7fb94c3 100644 --- a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md +++ b/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md @@ -190,7 +190,7 @@ To run the CL, use a similar command structure as described for running EukPhylo | --contamination_loop | yes | seq, clade | The mode in which to run the CL | none | | --nloops | no | any positive integer | Number of iterations | 5 | -You can also change the tree-building method using the `--cl_tree_method` argument (`iqtree`, `iqtree_fast`, or `fasttree`). You can choose whether to run Guidance between each iteration, or just MAFFT, by using the `--cl_alignment_method` argument (`mafft_only` or `guidance`). Here are some mode-specific arguments: +You can also change the tree-building method using the `--cl_tree_method` argument (`iqtree`, `iqtree_fast`, `fasttree` or `raxml` with the default being `iqtree_fast`). You can choose whether to run Guidance between each iteration, or just MAFFT, by using the `--cl_alignment_method` argument (`mafft_only` or `guidance` with the default being `mafft_only`). Here are some mode-specific arguments: #### Sisters/subsisters mode