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

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.

Keywords: bioinformatics; phylogenetics; phylogenomics.

Figure 1.

Distribution of identified FliT genes across 5550 bacterial genomes (a total of 521 genomes had at least one copy of the gene identified within it, indicated by blue branches). Numbers in parentheses represent number of genomes of the total within each major clade that had at least one copy detected.

Figure 2.

Placing a newly recovered Alteromonas MAG into a phylogenomic context by providing GToTree solely NCBI accessions for the references and a fasta file of the newly recovered MAG. MAG indicates metagenome-assembled genome.