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

MotivationPhylogenetic 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 developed getphylo, a tool to automatically generate multi-locus phylogenetic trees from GenBank files. It has a low barrier to entry with minimal dependencies. getphylo uses a parallelised, heuristic workflow to keep runtime and system requirements as low as possible. getphylo consistently produces trees with topologies comparable to other tools in less time. Furthermore, as getphylo does 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 makes getphylo a valuable addition to the phylogenetics toolkit. Availabilitygetphylo is 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).