Link Search Menu Expand Document

OrthoFinder

OrthoFinder is a program for phylogenetic orthology inference. It can be installed using the orthofinder.yml virtual environment using conda.

Running OrthoFinder to find orthologs between sets of FASTA amino acid sequences

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…

  1. -t sets the number of threads/processors to use (n).
  2. -S is used to select the search tool OrthoFinder uses. Setting it to diamond is far faster than the default BLAST method.
  3. -f is 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.

See also

Further reading