From d4093f8f128dad41600b7d973355c188a6454742 Mon Sep 17 00:00:00 2001
From: "Adri K. Grow" <42044618+adriannagrow@users.noreply.github.com>
Date: Tue, 28 Jan 2025 14:46:23 -0500
Subject: [PATCH] Updated QuickStart EukPhylo (markdown)

---
 QuickStart-EukPhylo.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md
index c2ffb0c..96e7990 100644
--- a/QuickStart-EukPhylo.md
+++ b/QuickStart-EukPhylo.md
@@ -110,7 +110,8 @@ If a user choose to use their own gene families database, they need to replace t
 
 
 ## Set Up:
-* A folder called “Scripts” containing all the [scripts from Github](https://github.com/Katzlab/EukPhylo/tree/main/PTL2/Scripts)
+### Structure:
+* A folder called “Scripts” with scripts from [here](https://github.com/Katzlab/EukPhylo/tree/main/PTL2/Scripts) on Github
  * Inside the Scripts folder, you also need to add the trimal-trimAl and guidance.v2.02 folders, as downloaded from [here](http://trimal.cgenomics.org/downloads) and [here](https://github.com/anzaika/guidance)
 * An empty output folder named as you wish for all output files (which will include trees and guidance files when done running), for example: Output_folder
 * A folder called “OutgroupR2Gs” containing the amino acid (AA) ReadyToGo fasta files for your target and outgroup taxa listed in your taxon_list.txt