From 88968d7a90ca73bf35c729054daf95a3b01476ba Mon Sep 17 00:00:00 2001
From: MCLeleu <123706003+MCLeleu@users.noreply.github.com>
Date: Tue, 13 Aug 2024 10:09:54 -0400
Subject: [PATCH] Updated PhyloToL Part 2: MSAs, trees, and contamination loop
 (markdown)

---
 PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
index c677856..153b7e5 100644
--- a/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
+++ b/PhyloToL-Part-2:-MSAs,-trees,-and-contamination-loop.md
@@ -115,6 +115,9 @@ Argument | Default | Choices | Help
 --sim_taxa | None |   | Path to the file with the taxa (10-digit codes) to apply the similarity filter on.
 
 Core parameters - rarely changed from defaults
+
+Argument | Default | Choices | Help
+-- | -- | -- | --
 --blast_cutoff | 1e-20 |   | Blast e-value cutoff.
 --len_cutoff | 10 |   | Amino acid length cutoff for removal of very short sequences after column removal in Guidance.
 --similarity_filter | store_true |   | Run the similarity filter in pre-Guidance.