OrthoFinder
From Wikipedia, the free encyclopedia
OrthoFinder is a command-line software tool for comparative genomics.[1][2] 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.
| OrthoFinder | |
|---|---|
| Original authors | David Emms Steven Kelly |
| Developer | David Emms |
| Initial release | 2015 |
| Written in | Python |
| Operating system | Linux |
| Type | Bioinformatics |
| License | GNU GPL v3 |
| Website | github |
| Repository | github |
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 2021, the tool has been referenced by more than 1500 published studies.[3]