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Updated PhyloToL Part 1 (markdown)

Katzlab 2024-08-09 17:28:28 -04:00
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PhyloToL-Part-1.md

@ -58,18 +58,9 @@ PhyloToL6 is designed to have an interchangeable hook. As the Hook database is r
###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
* 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
* 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