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 the package, and for details on 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

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.