Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis

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 s...

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Veröffentlicht in:Journal of molecular evolution
Hauptverfasser: Schoenstein, Martin, Mermillod, Pauline, Kress, Arnaud, Lecompte, Odile, Nevers, Yannis
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Germany 29.10.2025
Schlagworte:
Comparative genomics
Phylogenetic profiling
Coevolution
Python package
ISSN:0022-2844, 1432-1432, 1432-1432
Online-Zugang:Volltext
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Zusammenfassung: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 Profylo to benchmark their ability to predict functional relationships between human genes, using different datasets. Finally, we demonstrate the utility of the package with an example case study of the presence-absence of all protein-coding genes in the human genome. Profylo is available on GitHub at https://github.com/MartinSchoenstein/Profylo .
Bibliographie:ObjectType-Article-1
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ISSN:0022-2844
1432-1432
1432-1432
DOI:10.1007/s00239-025-10280-6