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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 not cover an alternative pipeline (which you could use outside the workshop) 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