From bb04f21cda63178165c4dc4c72ef48e1fcc1ecfa Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Wed, 22 Jan 2025 13:03:46 -0500
Subject: [PATCH] Updated EukPhylo Part 2: MSAs, trees, and contamination loop
 (markdown)

---
 EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md b/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md
index 6a950d9..b7692c7 100644
--- a/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md
+++ b/EukPhylo-Part-2:-MSAs,-trees,-and-contamination-loop.md
@@ -18,6 +18,7 @@ The following are required to run EukPhylo part 1. The dependencies are confirme
     * [ETE3](http://etetoolkit.org/) (version 3.1.2.)
     * [tqdm](https://tqdm.github.io/) (version 4.66.4; unlikely to matter)
 * [Guidance](https://taux.evolseq.net/guidance/) (version 2.0.2)
+    * Note that once you have downloaded Guidance, you will likely have to run the command [chmod u+x](https://www.computerhope.com/unix/uchmod.htm) on the guidance executable script (found within the www folder) as well as all dependency executable scripts (found within the programs folder).
 * [TrimAL](https://vicfero.github.io/trimal/index.html) (version 2.rev0)
 * [MAFFT](https://mafft.cbrc.jp/alignment/software/) (version 7.49)
 * [IQ-Tree](http://www.iqtree.org/) (version 2.1.2) and/OR [RAxML](https://cme.h-its.org/exelixis/web/software/raxml/) (version 8.2.12) and/OR [FastTree](https://microbesonline.org/fasttree/) (version 2.1)