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Updated PhyloToL Part 1 (markdown)

Katzlab 2024-08-09 17:51:02 -04:00
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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 ### Swapping out the hook
Replacing the PhyloToL Hook DB with a user-defined set of gene families is straightforward: 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) * 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 of output>.dmnd`)
* The hook then is put in the db_OG database folder prior to running Part 1 * 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`