Applications and Considerations of GToTree: A User-Friendly Workflow for Phylogenomics

Evolutionary Bioinformatics Online
Michael D Lee

Abstract

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 researchers the capability to generate phylogenomic trees to help guide their work. This commentary describes two common applications where GToTree can be helpful and then discusses some things to consider when using the program.

References

Jun 10, 2009·Bioinformatics·Salvador Capella-GutiérrezToni Gabaldón
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Nov 1, 2011·PLoS Computational Biology·Sean R Eddy
Jul 17, 2012·Bioinformatics·Doug HyattEdward C Uberbacher
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Aug 28, 2018·Nature Biotechnology·Donovan H ParksPhilip Hugenholtz
Oct 26, 2018·Nucleic Acids Research·Sara El-GebaliRobert D Finn
Mar 14, 2019·Bioinformatics·Michael D Lee
Apr 2, 2019·Nucleic Acids Research·Ivica Letunic, Peer Bork

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Citations

Dec 14, 2019·Cell·Maria G PachiadakiRamunas Stepanauskas

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Software Mentioned

anvi
iToL
GToTree
TaxonKit
TREE
IQ
Interactive Tree of Life 13 ( iToL )
GTDB
Tk
Alteromonas

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