OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplication events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format.
The following software has been designed to work in concert with OrthoFinder or to make use of OrthoFinder analyses
Clust: Automatic extraction of optimal co-expressed gene clusters from gene expression data
OrthoFiller: An automated method for detecting and correcting false negative genome annotation errors.
OMGene: a method for detecting and correcting erroneous gene models by optimizing evolutionary consistency
STRIDE: Species Tree Root Inference from gene Duplicaiton Events
If you use OrthoFinder in your work please cite:
Emms, D. and Kelly, S. (2015). OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biology 16: 157
Emms, D. and Kelly, S. (2019). OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20: 238