OrthoFinder Tutorials Phylogenetic orthology inference for comparative genomics


OrthoFinder is a software program for phylogenetic orthology inference.

OrthoFinder workflow

It takes as input the proteomes for the species you want to analyse and from these it automatically:

As well as large scale analyses, it can be used to carefully check individual ortholog relationships prior to experimental studies.

OrthoFinder vs OrthoMCL and other orthology inference software

Unlike other orthology inference software OrthoFinder uses gene trees. This means you can check every ortholog relationship in the gene tree it came from. The use of gene trees gives very high ortholog inference accuracy:

Quest for Orthologs benchmarks

Despite OrthoFinder using a more rigorous, gene-tree based approach to ortholog inference it is incredibly fast! In addition to this, it also returns far more comparative genomics data than other methods (orthogroups, orthologs, rooted genes trees, gene duplication events etc.)

Runtime on sets of Fungi species using 16 cores

OrthoFinder citation

OrthoFinder’s orthogroup and ortholog inference are described here:

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

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

If you use the OrthoFinder species tree then also cite:

Emms D.M. & Kelly S. STRIDE: Species Tree Root Inference from Gene Duplication Events (2017), Mol Biol Evol 34(12): 3267-3278

Emms D.M. & Kelly S. STAG: Species Tree Inference from All Genes (2018), bioRxiv https://doi.org/10.1101/267914