Members of the McTavish Lab focus on developing efficient methods that take advantage of the novel information in large scale data sets, with an emphasis on reproducibility and open science.

Current projects:

  • Extensiphy: Placing taxa in a sequence alignment and phylogeny using Next Generation Sequencing reads

Testing the effects of choice of reference genome and SNP calling pipeline parameters on phylogenetic inference.

Github repo

  • TreeToReads: Simulating pipelines to generate Next Generation Sequencing reads from realistic phylogenies

GitHub repo


  • Physcraper: Automated phylogenetic updating

Physcraper GitHub repo Documentation Examples


  • The Open Tree of Life

    A synthetic phylogenetic tree of all life. Drawing Drawing

UC Merced writup of recent Open Tree of life grant

PNAS paper Washington post article

Reddit ‘Ask-Me-Anything’