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PhyloNetworks.jl

PhyloNetworks is a Julia package with core utilities for phylogenetic networks. Phylogenetic networks represent the evolutionary relationships between a set of organisms, e.g. populations, species, languages, cultures etc. They provide an explicit representation of splitting events (when populations diverge from one another) and of merging events (when populations mix together due to migration of individuals, hybridization, polyploidization, recombination, etc.). Phylogenetic networks are called admixture graphs in population genetics, when merging events are interpreted as admixture between populations. They can also summarize ancestral recombination graphs.

PhyloNetworks is a core package that supports reading, writing, manipulating phylogenetic networks, and other standard tools. It is used by other packages for more specialized tasks, such as

  • PhyloPlots to visualize phylogenetic networks,
  • SNaQ for the inference of phylogenetic networks from quartet concordance factors (qCF),
  • QuartetNetworkGoodnessFit to calculate quartet concordance factors expected from a general network and test the adequacy of a network to qCF data,
  • PhyloTraits for the inference of trait evolution along a phylogenetic network,
  • PhyloCoalSimulations to simulate gene trees under a coalescent process along a phylogenetic networks.

How to get help

  • the package wiki has a step-by-step tutorial, done for the MBL workshop (last revised 2022), with background on networks and explanations.
  • tutorial for comparative methods, including network calibration (2023 workshop)
  • the google group has answers to common questions.
  • the Manual and below has a quick tutorial (navigation on the left).
  • the Library further below has the full list of documented functions.

References

See their bibtex format.

for the package in particular, please cite:

Manual

Library

For help on individual functions, see the library: