From f92266464117a5a4b3614f34770e10883b1d3dc0 Mon Sep 17 00:00:00 2001
From: "Adri K. Grow" <42044618+adriannagrow@users.noreply.github.com>
Date: Mon, 3 Feb 2025 11:54:17 -0500
Subject: [PATCH] Updated QuickStart EukPhylo (markdown)

---
 QuickStart-EukPhylo.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md
index a8458b9..86c5744 100644
--- a/QuickStart-EukPhylo.md
+++ b/QuickStart-EukPhylo.md
@@ -136,8 +136,8 @@ For additional input parameter options, see table below or run: `python phylotol
 |`--end`|choices = `unaligned`, `aligned`, `trees`|Stage until which to run PhyloToL. Options are `unaligned` (which will run up to but not including guidance), `aligned` (which will run up to but not including RAxML), and `trees` which will run through RAxML')|default = `trees`|
 |`--gf_list`|Path to the file with the GFs of interest. Only required if starting from the raw dataset|default = None|
 |`--taxon_list`|Path to the file with the taxa (10-digit codes) to include in the output|default = None| 
-|`--data`|Path to the input dataset. The format of this varies depending on your --start parameter. If you are running the contamination loop starting with trees, this folder must include both trees AND a fasta file for each tree (with identical file names other than the extension) that includes an amino-acid sequence for each tip of the tree (with the sequence names matching exactly the tip names)|default = None|
-|`--output`|Directory where the output folder should be created. If not given, the folder will be created in the parent directory of the folder containing the scripts|default = `../`|
+|`--data`|Path to the input dataset. The format of this varies depending on your --start parameter. If you are running the contamination loop starting with trees, this folder must include both trees AND a fasta file for each tree (with identical file names other than the extension) that includes an amino-acid sequence for each tip of the tree (with the sequence names matching exactly the tip names)||default = None|
+|`--output`|Directory where the output folder should be created. If not given, the folder will be created in the parent directory of the folder containing the scripts||default = `../`|
 
 
 ### Modularity of options