Journal
BIOINFORMATICS
Volume 35, Issue 20, Pages 4162-4164Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btz188
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Funding
- NASA Space Biology [NNH16ZTT001N-MOBE]
- NASA's Planetary Science Division (Astrobiology Program)
- NSF [ACI-1548562]
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Genome-level evolutionary inference (i.e. phylogenomics) is becoming an increasingly essential step in many biologists' work. Accordingly, there are several tools available for the major steps in a phylogenomics workflow. But for the biologist whose main focus is not bioinformatics, much of the computational work required-such as accessing genomic data on large scales, integrating genomes from different file formats, performing required filtering, stitching different tools together etc.-can be prohibitive. Here I introduce GToTree, a command-line tool that can take any combination of fasta files, GenBank files and/or NCBI assembly accessions as input and outputs an alignment file, estimates of genome completeness and redundancy, and a phylogenomic tree based on a specified single-copy gene (SCG) set. Although GToTree can work with any custom hidden Markov Models (HMMs), also included are 13 newly generated SCG-set HMMs for different lineages and levels of resolution, built based on searches of similar to 12 000 bacterial and archaeal high-quality genomes. GToTree aims to give more researchers the capability to make phylogenomic trees.
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