OrthoFinder Tutorials Phylogenetic orthology inference for comparative genomics

A2. Getting OrthoFinder input data

Proteomes may be available in a number of places. The (Running an example OrthoFinder analysis) showed how to download data from Ensembl, here are a few pointers for other popular websites.


  1. You’ll first need to create an account and log in.

  2. Go to the download section:

  3. Select the _primaryTranscriptOnly.fa.gz files for each species you want.

  4. Go to the top of the page, and click “Download Selected Files”. They’ll be in a package with the original directory structure so you’ll have to get each of the files, put them in a single file and gunzip them. You don’t need to run the primary_transcript.py script on them as Phytozome has already done that step.


Let me know if you think pointers to any other sites would be helpful.