Software:OrthoFinder
| Original author(s) | David Emms Steven Kelly |
|---|---|
| Developer(s) | David Emms Yi Liu Laurence Belcher Jonathan Holmes |
| Initial release | 2015 |
| Repository | github |
| Written in | Python |
| Operating system | Linux |
| Type | Bioinformatics |
| License | GNU GPL v3 |
| Website | github |
OrthoFinder is a command-line software tool for comparative genomics.[1][2][3] OrthoFinder determines the correspondence between genes in different organisms (also known as orthology analysis). This correspondence provides a framework for understanding the evolution of life on Earth, and enables the extrapolation and transfer of biological knowledge between organisms. In 2026 OrthoFinder was updated to run in linear time with an enhanced scalability workflow by assiging new sequences to an existing OrthoFinder run, representing a major change to the underlying algorithm.[3]
OrthoFinder takes FASTA files of protein sequences as input (one per species) and as output provides:
- Orthogroups
- Rooted Phylogenetic trees of all orthogroups
- A rooted species tree for the set of species included in the input dataset
- Hierarchical orthogroups for each node in the species tree
- Orthologs between all species
- Gene duplication events mapped to branches in the species tree
- Comparative genomic statistics
As of August 2026, the tool has been referenced by more than 10,000 published studies.[4]
See also
References
- ↑ Emms, David M; Kelly Steven (2015). "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy". Genome Biology 16 (157): 157. doi:10.1186/s13059-015-0721-2. PMID 26243257.
- ↑ Emms, David M; Kelly Steven (2019). "OrthoFinder: phylogenetic orthology inference for comparative genomics". Genome Biology 20 (238): 238. doi:10.1186/s13059-019-1832-y. PMID 31727128.
- ↑ 3.0 3.1 Emms, David M.; Liu, Yi; Belcher, Laurence; Holmes, Jonathan; Kelly, Steven (2026). "OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability" (in en). Nature Methods 23 (7): 1327–1333. doi:10.1038/s41592-026-03126-6. ISSN 1548-7105. https://www.nature.com/articles/s41592-026-03126-6.
- ↑ "Citations for Emms & Kelly 2015". https://scholar.google.com/scholar?hl=en&as_sdt=0%2C5&q=orthofinder&btnG=.
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