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Welcome to the GToTree wiki!

GToTree is a user-friendly workflow for phylogenomics intended to give more researchers the capability to create phylogenomic trees and to make the process of iterating phylogenomic trees much easier. The open-access Bioinformatics Journal publication is available here. GToTree can be installed and run on a Mac or Linux machine, as well as on Windows within a Windows Subsystem for Linux environment 👍

For an overview of what this is all about, see the "What is GToTree?" page. Or, to see some practical ways GToTree can be helpful, scan through the Example usage page.

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A quick conda installation can be run like so:

# installing mamba if needed first (for faster conda installs)
conda install -n base -c conda-forge mamba
mamba create -y -n gtotree -c astrobiomike -c conda-forge -c bioconda -c defaults gtotree

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Wiki contents

• What is GToTree?
• Installation
  • Conda Quickstart!
  • Updating to a newer version
  • Installation without Conda
• Example usage
  • Alteromonas example
  • Using GToTree with the Genome Taxonomy Database (GTDB)
  • Visualization of gene-presence/absence across Bacteria
  • Tree-of-Life example
  • Using the alignment and partitions file with another program
• User Guide
  • Required inputs
  • Outputs
  • Optional arguments and parameters
  • Options set for programs run
  • Genome completeness and redundancy estimations
  • All programs used citation info
• Single-copy gene-sets
  • Code
• Things to consider
  • An important caveat on the idea of a workflow for phylogenomics
  • When to use GToTree and when not
    • Is GToTree useful for assigning taxonomy?
    • Should GToTree be used for estimating genome/MAG/bin completeness?
  • Consider using "representative" genomes
  • Working with many genomes
  • Filtering genes by length
  • Filtering genomes by hits to targets
  • Best-hit mode
  • Eukaryotes with GToTree?

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