From 93d70c015374a4367ce85158a13a5d0b707791e0 Mon Sep 17 00:00:00 2001
From: Katzlab <katzlab@smith.edu>
Date: Fri, 9 Aug 2024 17:36:42 -0400
Subject: [PATCH] Updated PhyloToL Part 1 (markdown)

---
 PhyloToL-Part-1.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/PhyloToL-Part-1.md b/PhyloToL-Part-1.md
index 1be1d40..e48ce0e 100644
--- a/PhyloToL-Part-1.md
+++ b/PhyloToL-Part-1.md
@@ -58,9 +58,9 @@ Users can either use the PhyloToL Hook database or a set of gene families of int
 
 
 ### Swapping out the hook
-What to know about using your own hook:
-* You will need two files, a fasta file with your target sequences, and this same file reformatted as a diamond database (diamond makedb --in <path to fasta file> -d <name you want to give it>.dmnd)
-* The hook lives in the db_OG database folder
+Replacing the PhyloToL Hook DB with a user-defined set of gene families is straightforward:
+* You need two files, a fasta file with your target sequences, and this same file reformatted as a diamond database (diamond makedb --in <path to fasta file> -d <name you want to give it>.dmnd)
+* The hook then is put in the db_OG database folder prior to running Part 1
 * Be aware that you must give your fasta file and your diamond file the same exact prefix, or else your run will fail at the end. For example, the Katzlab Hook-6.6 files are named: Hook-6.6.fasta, Hook-6.6.dmnd