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Cecile Ane edited this page Jul 6, 2018 · 3 revisions

Welcome to the PhyloNetwork software workshop! This site has material for a software workshop on phylogenetic networks at the 2018 MBL workshop on molecular evolution (earlier version for a 2016 workshop). It covers steps to go from a bunch of multiple alignments (aligned gene sequences, or loci) to a phylogenetic network displaying the relationships between the species in the alignments

topics covered

  • example data to download
  • TICR pipeline overview: from sequences to quartet concordance factors (CFs, proportion of genes having a particular history)
  • PhyloNetworks for network estimation: from quartet CFs or gene trees to phylogenetic networks, and bootstrap analysis to understand network uncertainty
  • TICR test: is a population tree with ILS sufficient (vs network)?

more details

  • TICR pipeline

    • analyze each locus with MrBayes
    • do a concordance analysis with BUCKy on each set of 4 taxa
    • summarize all quartet concordance factors (CFs)
    • estimate a species tree using Quartet MaxCut

    We will also cover an alternative pipeline to

    • analyze each locus with RAxML, including bootstrap
    • estimate a species tree with ASTRAL
  • Julia package PhyloNetworks with SNaQ (Species Network applying Quartets)

    • read the quartet concordance factors
    • estimate a phylogenetic network
    • choose the number of reticulations
    • run a bootstrap analysis
    • plot bootstrap support for tree edges, and for hybridizations
  • TICR test in the R package phylolm (Testing Incongruence Checking in R)

    • test if a population tree with the coalescent (ILS only) is adequate to explain the quartet concordance factors
    • identify taxa involved in outlier quartets