getphylo: rapid and automatic generation of multi-locus phylogenetic trees

Abstract

AbstractMotivationPhylogenetic trees are the primary tool for visualising evolutionary relationships. Traditionally, phylogenies are inferred from manually curated sets of marker genes. As available genomic data increases, there is increasing demand for tools to automatically build phylogenies from assembled genomes. Existing tools rely on reference databases of preselected marker genes, limiting their taxonomic scope. We sought to develop a tool that could quickly build phylogeny from input genomes alone.ResultsWe developedgetphylo, a tool to automatically generate multi-locus phylogenetic trees from GenBank files. It has a low barrier to entry with minimal dependencies.getphylouses a parallelised, heuristic workflow to keep runtime and system requirements as low as possible.getphyloconsistently produces trees with topologies comparable to other tools in less time. Furthermore, asgetphylodoes not rely on reference databases, it has a virtually unlimited scope in terms of taxonomy (e.g., not limited to bacteria) and genetic scale (e.g., can analyse plasmids, prophage, and gene clusters). This combination of speed and flexibility makesgetphyloa valuable addition to the phylogenetics toolkit.Availabilitygetphylois freely available and is downloadable through the Python Package Index (pip install getphylo;https://pypi.org/project/getphylo/) and GitHub (https://github.com/drboothtj/getphylo).