OrthoFinder

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 author(s)	David Emms Steven Kelly
Developer(s)	David Emms
Initial release	2015
Repository	github.com/davidemms/OrthoFinder/releases
Written in	Python
Operating system	Linux
Type	Bioinformatics
License	GNU GPL v3
Website	github.com/davidemms/OrthoFinder

OrthoFinder workflow and outputs.

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]

See also

• Bioinformatics
• Homology (biology)
• Sequence homology
• Protein family
• Sequence clustering