Orthology clusters from gene trees with possvm

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  • dc.contributor.author Grau Bové, Xavier
  • dc.contributor.author Sebé-Pedrós, Arnau
  • dc.date.accessioned 2021-12-01T07:35:45Z
  • dc.date.available 2021-12-01T07:35:45Z
  • dc.date.issued 2021
  • dc.description.abstract Possvm (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.
  • dc.description.sponsorship Research in A.S.-P. group was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme Grant Agreement (851647), the Spanish Ministry of Science and Innovation (PGC2018-098210-A-I00), the Centro de Excelencia Severo Ochoa scheme (SEV-2016-0571), and the Agencia Estatal de Investigación. X.G.-B. was supported by a Juan de la Cierva fellowship (FJC2018-036282-I) from the Spanish Ministry of Economy, Industry, and Competitiveness.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Grau-Bové X, Sebé-Pedrós A. Orthology clusters from gene trees with possvm. Mol Biol Evol. 2021;38(11):5204-8. DOI: 10.1093/molbev/msab234
  • dc.identifier.doi http://dx.doi.org/10.1093/molbev/msab234
  • dc.identifier.issn 0737-4038
  • dc.identifier.uri http://hdl.handle.net/10230/49115
  • dc.language.iso eng
  • dc.publisher Oxford University Press
  • dc.relation.ispartof Mol Biol Evol. 2021;38(11):5204-8
  • dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/851647
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PGC2018-098210-A-I00
  • dc.rights © 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.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri https://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Comparative genomics
  • dc.subject.keyword Gene phylogenetics
  • dc.subject.keyword Orthology inference
  • dc.title Orthology clusters from gene trees with possvm
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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