OrthoFinder

OrthoFinder is open-source software for comparative genomics that infers orthology relationships across multiple species. It identifies orthogroups—groups of genes descended from a single gene in the last common ancestor—and derives orthologs and paralogs, gene trees, and a species tree. The pipeline is designed to be automated and scalable to large sets of genomes, making it a popular choice for functional annotation transfer and evolutionary studies.

The typical workflow begins with an all-versus-all sequence similarity search among the input protein sequences, using DIAMOND, BLAST, or MMseqs2. The results are clustered into orthogroups with MCL. For each orthogroup, a gene tree is inferred, and these trees are reconciled to infer orthology and paralogy relationships. OrthoFinder can infer a rooted species tree using the STAG and STRIDE algorithms and provides outputs including orthogroups, gene trees, orthologous and paralogous relationships, and a species tree. It also reports gene duplication events and supports visualization of the results.

OrthoFinder was introduced by Emms and Kelly and has undergone major updates in its second generation, OrthoFinder2, which improved accuracy and added built-in species-tree inference and compatibility with fast sequence-search tools. The software is widely used in comparative genomics to study gene family evolution, to transfer functional annotations across species, and to examine evolutionary relationships among organisms.