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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. The open-access Bioinformatics Journal publication is available here.

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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See the conda quickstart installation page to have things up and running in just a single step!

conda 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
  • Eukaryotes with GToTree?

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