TreeProfiler: A command-line tool for computing and visualizing phylogenetic profiles against large trees

Abstract

Phylogenetic profiling is a common bioinformatics approach used to study the distribution of traits across species or, more broadly, along the topology of a phylogenetic tree. Originally proposed as a technique for establishing functional relationships between various genes through their correlated presence/absence patterns, phylogenetic profiling is currently considered a powerful exploration tool for investigating the evolutionary distribution of nearly any trait across both gene or species phylogenies. However, computing and visualizing phylogenetic profiles based on large trees is a laborious task. First, traits need to be mapped against tree nodes, which usually requires the implementation of ad hoc scripts or substantial manual work. Second, tree mapping is often limited to leaf nodes, neglecting the usefulness of profiling traits against internal tree nodes. Lastly, graphical exploration of large phylogenetic tree-based profiles is challenging, as plotting usually requires complex manual adjustments and most visualization tools cannot scale to the size and complexity of current datasets. To address these limitations, we have developed TreeProfiler, a command line tool designed to facilitate both the automated annotation of large trees using a wide range of data sources, and the visual exploration of these annotations as phylogenetic profiles. TreeProfiler enables seamless annotation of massive trees and data tables, including built-in support for functional data, taxonomic information, multiple sequence alignments and protein domain architectures. Importantly, TreeProfiler expands its annotation capabilities beyond tree leaves, enabling the annotation of internal nodes with summarized or consensus information under each branch. Additionally, TreeProfiler offers a predefined set of graphical layouts that are based on the ETE Toolkit v4.0 library. TreeProfiler offers unique capabilities that extend and facilitate the use of phylogenetic profiling techniques for a broad landscape of scenarios and for a wide community of researchers interested in evolutionary analysis. To demonstrate its value, we showcase TreeProfiler by automatically profiling multiple data sources across a large bacterial phylogeny including 45,555 species, and by exploring functional and taxonomic annotations over a large gene family tree. TreeProfiler is available at https://github.com/compgenomicslab/TreeProfiler.