PhyloNetworks is a Julia package for the manipulation, visualization, inference of phylogenetic networks, and their use for trait evolution.

How to get help

  • the package wiki has a step-by-step tutorial, done for the 2019 MBL workshop, with background on networks and explanations.
  • the google group has answers to common questions.
  • the Manual below has a quick tutorial (navigation on the left).
  • the Library and and Index further below has the full list of documented functions.


See their bibtex format.

for the package:

for trait evolution:

  • Teo, Rose, Bastide & Ané (2022). Accounting for intraspecific variation in continuous trait evolution on a reticulate phylogeny. bioRxiv
  • Karimi, Grover, Gallagher, Wendel, Ané & Baum (2020). Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae). Systematic Biology, 69(3):462-478. doi:10.1093/sysbio/syz073.
  • Bastide, Solís-Lemus, Kriebel, Sparks, Ané (2018). Phylogenetic Comparative Methods for Phylogenetic Networks with Reticulations. Systematic Biology, 67(5):800–820. doi:10.1093/sysbio/syy033.

for network inference: