From 5f100177d421dc93f22692294e30252e47d23a68 Mon Sep 17 00:00:00 2001 From: "Godwin N. Ani" Date: Thu, 17 Jul 2025 14:51:37 -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 7171aa5..ef7ba86 100644 --- a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md +++ b/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md @@ -135,7 +135,7 @@ Argument | Default | Choices | Description ## Gene trees -After homology assessment and building MSAs (the Guidance step), EukPhylo trims alignments and build trees. By default, alignments are trimmed at 0.95% with TrimAL, and trees by default are built by IqTREE with an LG+G model; users may choose to use a different third-party tool for phylogenetic reconstruction. +After homology assessment and building MSAs (the Guidance step), EukPhylo trims alignments and build trees. By default, columns in the alignments are trimmed at 70% gaps with TrimAL, and trees by default are built by IqTREE with an LG+G model; users may choose to use a different third-party tool for phylogenetic reconstruction. Argument | Default | Choices | Description -- | -- | -- | --