Applications and Considerations of GToTree: A User-Friendly Workflow for Phylogenomics.
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ABSTRACT:
SUBMITTER: Lee MD
PROVIDER: S-EPMC6659180 | biostudies-literature | 2019
REPOSITORIES: biostudies-literature
Publications
Applications and Considerations of GToTree: A User-Friendly Workflow for Phylogenomics.
Evolutionary bioinformatics online 20190725
Phylogenomics is the practice of attempting to infer evolutionary relationships at a genome-level. This is becoming a standard step in the characterization of newly recovered genomes and to direct/constrain further research; yet the process from start to finish of building a de novo phylogenomic tree that is specific to the organisms of interest can still be computationally intractable for many biologists. GToTree is a recently published user-friendly workflow for phylogenomics intended to give ...[more]
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Project description:SummaryGenome-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 ∼12 000 bacterial and archaeal high-quality genomes. GToTree aims to give more researchers the capability to make phylogenomic trees.Availability and implementationGToTree is open-source and freely available for download from: github.com/AstrobioMike/GToTree. It is implemented primarily in bash with helper scripts written in python.Supplementary informationSupplementary data are available at Bioinformatics online.
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2013-06-13 | GSE40748 | GEO
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2013-06-13 | E-GEOD-40748 | biostudies-arrayexpress
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