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 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 .