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STRIDE: Species Tree Root Inference from Gene Duplication Events

The correct interpretation of a phylogenetic tree is dependent on it being correctly rooted. STRIDE takes an unrooted species tree and a set of unrooted gene trees and identifies well-supported gene duplication events within the gene trees to infer the root of the species tree.

A gene duplication event at the base of a clade of species is synapamorphic, and thus excludes the root of the species tree from that clade. STRIDE is a fast, effective, and outgroup-free method for species tree root inference from gene duplication events. On test datasets on a typical 4 core desktop it analysed 14,454 gene trees covering 47 species in ~25s.

Test datasets together with a script to run all the datasets can be downloaded from DOI.

Usage:

STRIDE requires python plus numpy, scipyt and the ete (version 2 or 3) tree library. To run STRIDE:

stride.py -s gene_to_species_conversion -S Species_tree.tre -d gene_trees/

Stride needs to be able to map the genes in the gene trees to the species in the species tree. Gene names in the gene trees should start with the name of the species they come from. Use the -s option to tell stride how to do the mapping:

  • dot: SpeciesName.GeneName -> SpeciesName

  • dash: SpeciesName_GeneName -> SpeciesName

  • second_dash: Species_Name_GeneName -> Species_Name

  • 3rd_dash: Species_X_Name_GeneName -> Species_X_Name