OrthoFinder: phylogenetic orthology inference for comparative genomics

TLDR

The paper introduces a major advance to the OrthoFinder method. The method extends OrthoFinder’s orthogroup inference to produce phylogenetic orthologs, rooted gene trees, duplication events, a rooted species tree, and comparative genomic statistics. Benchmarking on real and simulated data shows OrthoFinder matches or surpasses comparable methods, is the most accurate on the Quest for Orthologs benchmark, and delivers comprehensive phylogenetic analysis with speed and scalability comparable to the fastest heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder.

Abstract

Abstract Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted genes trees, gene duplication events, the rooted species tree, and comparative genomic statistics. Each output is benchmarked on appropriate real or simulated datasets and, where comparable methods exist, OrthoFinder is equivalent to or outperforms these methods. Furthermore, OrthoFinder is the most accurate ortholog inference method on the Quest for Orthologs benchmark test. Finally, OrthoFinder’s comprehensive phylogenetic analysis is achieved with equivalent speed and scalability to the fastest, score-based heuristic methods. OrthoFinder is available at https://github.com/davidemms/OrthoFinder .