Grau Bové, XavierSebé-Pedrós, Arnau2021-12-012021-12-012021Grau-Bové X, Sebé-Pedrós A. Orthology clusters from gene trees with possvm. Mol Biol Evol. 2021;38(11):5204-8. DOI: 10.1093/molbev/msab2340737-4038http://hdl.handle.net/10230/49115Possvm (Phylogenetic Ortholog Sorting with Species oVerlap and MCL [Markov clustering algorithm]) is a tool that automates the process of identifying clusters of orthologous genes from precomputed phylogenetic trees and classifying gene families. It identifies orthology relationships between genes using the species overlap algorithm to infer taxonomic information from the gene tree topology, and then uses the MCL to identify orthology clusters and provide annotated gene families. Our benchmarking shows that this approach, when provided with accurate phylogenies, is able to identify manually curated orthogroups with very high precision and recall. Overall, Possvm automates the routine process of gene tree inspection and annotation in a highly interpretable manner, and provides reusable outputs and phylogeny-aware gene annotations that can be used to inform comparative genomics and gene family evolution analyses.application/pdfeng© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.info:eu-repo/semantics/articlehttp://dx.doi.org/10.1093/molbev/msab234Comparative genomicsGene phylogeneticsOrthology inferenceinfo:eu-repo/semantics/openAccess