OrthoFinder can be used to find orthologs between sets of FASTA amino acid files as follows:
$ orthofinder -t n -S diamond -f path/to/fasta/files/
In this command…
-tsets the number of threads/processors to use (n).
-Sis used to select the search tool OrthoFinder uses. Setting it to
diamondis far faster than the default BLAST method.
-fis used to select the directory of FASTA amino acid sequences files you want to compare.
OrthoFinder will create a
Results directory (ending with the current month and day, e.g.
Results_Sep16/) in the target directory specified with
-f. This directory will contain summary statistics of orthologs found between the FASTA files, as well as putative gene duplication events, and phylogenetic trees of the detected orthogroups.