PhyloNetworks: analysis for phylogenetic networks
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.
- plot networks (and trees)
- 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
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