From ee9bb48a45d2c20073a2da0c0891d5967439774c Mon Sep 17 00:00:00 2001
From: "Adri K. Grow" <42044618+adriannagrow@users.noreply.github.com>
Date: Sun, 9 Feb 2025 01:33:13 -0500
Subject: [PATCH] Updated EukPhylo QuickStart (markdown)

---
 EukPhylo-QuickStart.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/EukPhylo-QuickStart.md b/EukPhylo-QuickStart.md
index be57d17..0646f33 100644
--- a/EukPhylo-QuickStart.md
+++ b/EukPhylo-QuickStart.md
@@ -148,12 +148,12 @@ Below are several optional ways to parameterize EukPhylo Part 2
 |Parameter|Options|Description|Default|
 |:---|:---|:---|:---|
 |`--blast_cutoff`|float|Blast e-value cutoff|`1e-20`
-|`--len_cutoff`|int|Amino acid length cutoff for removal of very short sequences after column removal in Guidance|10|
-|`--guidance_iters`|int|Number of Guidance iterations for sequence removal|5|
-|`--seq_cutoff`|float|During guidance, taxa are removed if their score is below this cutoff|0.3|
-|`--col_cutoff`|float|During guidance, columns are removed if their score is below this cutoff|0.0|
-|`--res_cutoff`|float|During guidance, residues are removed if their score is below this cutoff|0.0|
-|`--guidance_threads`|int|Number of threads to allocate to Guidance|20|
+|`--len_cutoff`|int|Amino acid length cutoff for removal of very short sequences after column removal in Guidance|`10`|
+|`--guidance_iters`|int|Number of Guidance iterations for sequence removal|`5`|
+|`--seq_cutoff`|float|During guidance, taxa are removed if their score is below this cutoff|`0.3`|
+|`--col_cutoff`|float|During guidance, columns are removed if their score is below this cutoff|`0.0`|
+|`--res_cutoff`|float|During guidance, residues are removed if their score is below this cutoff|`0.0`|
+|`--guidance_threads`|int|Number of threads to allocate to Guidance|`20`|
 
 **For reducing number of similar sequences:**
 |Parameter|Required|Options|Help|