{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Schoenstein M"],"funding":["Agence Nationale de la Recherche"],"pagination":["806-819"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12756282"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["93(6)"],"pubmed_abstract":["Phylogenetic profiling, involving the analysis of presence-absence of orthologs in a set of species, is a way to infer functional association between genes through co-evolutionary patterns. Since its inception, numerous methods have been described to construct phylogenetic profiles, evaluate their similarity, or identify clusters of co-evolving genes. However, few of these methods are available as downloadable software. We present Profylo, a phylogenetic profiling toolkit made available as an open-source Python 3.0 package. Profylo implements seven methods for comparing phylogenetic profiling, four algorithms for identification of co-evolving clusters, as well as tools to help with their analysis, including visualization features. We take advantage of the variety of methods implemented in "],"journal":["Journal of molecular evolution"],"pubmed_title":["Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis."],"pmcid":["PMC12756282"],"funding_grant_id":["ANR-24-CPJ1-0082-01"],"pubmed_authors":["Nevers Y","Mermillod P","Schoenstein M","Kress A","Lecompte O"],"additional_accession":[]},"is_claimable":false,"name":"Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis.","description":"Phylogenetic profiling, involving the analysis of presence-absence of orthologs in a set of species, is a way to infer functional association between genes through co-evolutionary patterns. Since its inception, numerous methods have been described to construct phylogenetic profiles, evaluate their similarity, or identify clusters of co-evolving genes. However, few of these methods are available as downloadable software. We present Profylo, a phylogenetic profiling toolkit made available as an open-source Python 3.0 package. Profylo implements seven methods for comparing phylogenetic profiling, four algorithms for identification of co-evolving clusters, as well as tools to help with their analysis, including visualization features. We take advantage of the variety of methods implemented in ","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Dec","modification":"2026-05-29T03:23:19.679Z","creation":"2026-05-29T03:13:08.933Z"},"accession":"S-EPMC12756282","cross_references":{"pubmed":["41160131"],"doi":["10.1007/s00239-025-10280-6"]}}