Gene

Comparative genomics

Tree (set theory)

Geodesy

Mathematical analysis

Genome

Artificial intelligence

Heuristic

Benchmark (surveying)

Genomics

Phylogenetic tree

Geography

Phylogenetic network

Inference

Mathematics

Computer science

Scalability

Genetics

Computational biology

Database

Evolutionary biology

Biology

Phylogenetics

Genome biology

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.

OrthoFinder: phylogenetic orthology inference for comparative genomics