Home - sungsik-kong/PhyNEST.jl GitHub Wiki

Welcome to the PhyNEST (Phylogenetic Network Estimation using SiTe patterns) wiki page!

PhyNEST is a julia package for inferring phylogenetic networks from genomic sequence data. This page contains materials for software workshop on phylogenetic networks and reticulate evolution at:

• Botany 2023: Methodological advances in reticulate evolution (Boise, ID., USA) (Slides)

Please see here for detailed documentation of PhyNEST.

The workshop covers steps to go from parsing input sequence alignment to estimating phylogenetic networks using PhyNEST. More specifically, we will walk through how to extract the quartet site pattern frequencies from the multiple sequence alignment, to use those site pattern frequencies to compute composite likelihood on a fixed topology, and to estimate the phylogenetic network that maximizes composite likelihood using two heuristics: hill climbing and simulated annealing.

• Download, install, and open julia.

  julia version >= 1.7 is recommended to use PhyNEST.

• In julia, install PhyNEST.

  • First, load Pkg, julia's built-in package manager (command: using Pkg)
  • Then, install PhyNEST (command: Pkg.add("PhyNEST"))
  • Load PhyNEST (command: using PhyNEST)
  • Check the installed version of PhyNEST (command: Pkg.status("PhyNEST")), just to make sure it is successfully installed
  • Close julia (command: exit())

  julia> using Pkg
  julia> Pkg.add("PhyNEST")
  julia> using PhyNEST
  julia> Pkg.status("PhyNEST")
      Status `~/.julia/environments/v1.7/Project.toml`
  [115de871] PhyNEST v0.1.10
  julia> exit()
  

• Download and install Dendroscope to visualize the network.

Sungsik Kong, David Swofford, and Laura Kubatko (2022) Inference of Phylogenetic Networks from Sequence Data using Composite Likelihood. Preprint available online on BioRxiv at https://doi.org/10.1101/2022.11.14.516468.

Please use google group to report bugs or post questions and/or suggestions.