From 914a3565958b78ad18c72469942a67312f916200 Mon Sep 17 00:00:00 2001 From: Katzlab Date: Fri, 9 Aug 2024 17:51:02 -0400 Subject: [PATCH] Updated PhyloToL Part 1 (markdown) --- PhyloToL-Part-1.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/PhyloToL-Part-1.md b/PhyloToL-Part-1.md index e48ce0e..bae2992 100644 --- a/PhyloToL-Part-1.md +++ b/PhyloToL-Part-1.md @@ -59,9 +59,9 @@ Users can either use the PhyloToL Hook database or a set of gene families of int ### Swapping out the hook 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 -d .dmnd) +* You need two files, a fasta file with your target sequences, and this same file reformatted as a diamond database (`diamond makedb --in -d .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 +* 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`