From edb28b4dc144b47f9b70953fb48e20e3ea67a109 Mon Sep 17 00:00:00 2001
From: "Adri K. Grow" <42044618+adriannagrow@users.noreply.github.com>
Date: Mon, 3 Feb 2025 11:58:22 -0500
Subject: [PATCH] Updated QuickStart EukPhylo (markdown)

---
 QuickStart-EukPhylo.md | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/QuickStart-EukPhylo.md b/QuickStart-EukPhylo.md
index 4f577c7..dcd94be 100644
--- a/QuickStart-EukPhylo.md
+++ b/QuickStart-EukPhylo.md
@@ -130,14 +130,14 @@ Basic running for building MSAs and Trees:
 
 For additional input parameter options, see table below or run: `python phylotol.py --help`
 
-|Flag|Options|Help|Default|
+|Flag|Options|Description|Default|
 |:---|:-------|:---|:---|
-|`--start`|choices = `raw`, `unaligned`, `aligned`, `trees`|Stage at which to start running PhyloToL|default = `raw`|
-|`--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 = `../`|
+|`--start`|`raw`, `unaligned`, `aligned`, `trees`|Stage at which to start running PhyloToL|`raw`|
+|`--end`|`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')|`trees`|
+|`--gf_list`||Path to the file with the GFs of interest. Only required if starting from the raw dataset|None|
+|`--taxon_list`||Path to the file with the taxa (10-digit codes) to include in the output|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)|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|`../`|
 
 
 ### Modularity of options