“OrthoFinder: phylogenetic orthology inference for comparative genomics” (2019), by David Emms et al. Genetics and Biochemistry research paper. Original abstract below, unchanged. A free PDF is available.

OrthoFinder: phylogenetic orthology inference for comparative genomics

David Emms, Steven L. Kelly · November 14, 2019 · Genetics and Biochemistry

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 gene trees, gene duplication events, the rooted species tree, and comparative genomics 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.

Free PDF DOI: 10.1186/s13059-019-1832-y