OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplication events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format.


Click here for links to downloads, install instructions and user manual

Click here for links to a set of tutorials on how to run and use OrthoFinder for your research

OrthoFinder integration

The following software has been designed to work in concert with OrthoFinder or to make use of OrthoFinder analyses

Clust: Automatic extraction of optimal co-expressed gene clusters from gene expression data

OrthoFiller: An automated method for detecting and correcting false negative genome annotation errors.

OMGene: a method for detecting and correcting erroneous gene models by optimizing evolutionary consistency

STRIDE: Species Tree Root Inference from gene Duplicaiton Events


If you use OrthoFinder in your work please cite:

Emms, D. and Kelly, S. (2015). OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology 16: 157

Emms, D. and Kelly, S. (2019). OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20: 238