A Julia package for statistical inference, data manipulation and visualization of phylogenetic networks
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README.md

PhyloNetworks: analysis for phylogenetic networks

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Overview

PhyloNetworks is a Julia package with utilities to:

  • read / write phylogenetic trees and networks, in (extended) Newick format. Networks are considered explicit: nodes represent ancestral species. They can be rooted or unrooted.
  • manipulate networks: re-root, prune taxa, remove hybrid edges, extract the major tree from a network, extract displayed networks / trees
  • compare networks / trees with dissimilarity measures (Robinson-Foulds distance on trees)
  • summarize samples of bootstrap networks (or trees) with edge and node support
  • estimate species networks from multilocus data (see below)
  • phylogenetic comparative methods for continuous trait evolution on species networks / trees
  • plot networks (and trees), via the companion package PhyloPlots

To get help, check

  • the latest documentation
  • the wiki for a step-by-step tutorial (June 2016) with background on networks
  • the google group for common questions. Join the group to post/email your questions, or to receive information on new versions, bugs fixed, etc.

If you use the package, please cite

  • Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017). PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution doi: 10.1093/molbev/msx235

Maximum pseudolikelihood estimation of species network: SNaQ

SNaQ implements the statistical inference method in Solís-Lemus and Ané (2016). The procedure involves a numerical optimization of branch lengths and inheritance probabilities and a heuristic search in the space of phylogenetic networks.

If you use SNaQ, please cite

  • Claudia Solís-Lemus and Cécile Ané (2016). Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting. PLoS Genet 12(3):e1005896. doi: 10.1371/journal.pgen.1005896

Phylogenetic comparative methods for trait evolution

For continuous traits, study based on the Brownian motion process, with or without transgressive evolution after reticulations: