Updated PhyloToL Part 1 (markdown)

PhyloToL-Part-1.md

@@ -54,6 +54,24 @@ And all of the CDS fasta files should be in a folder alongside the [Scripts](htt
 
 
 ## The Hook Database
+PhyloToL6 is designed to have an interchangeable hook. As the Hook database is replaceable and customizable, this step offers an opportunity to filter data for a group of gene families/functional groups of interest.
+
+###Swapping out the hook
+What to know about using your own hook:
+* 
+The hook lives in the Databases folder, specifically the db_OG folder
+* 
+The fasta file contains …..
+The diamond file contains …..
+It is recommended that you create your own diamond database using your fasta file, so you can be sure that diamond will be compatible with your computer’s version
+To do this, do the following command
+diamond makedb --in <path to fasta file> -d <name you want to give it>.dmnd
+Be aware that you must give your fasta file and your diamond file the same exact name, 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
+
+
 
 ## Processing transcriptomes