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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 level-1 phylogenetic networks.
To get help, check
- the latest SNaQ documentation
- the latest PhyloNetworks documentation
- PhyloUtilities with a step-by-step tutorial from multi-locus sequences to necessary input for SNaQ
- tutorial for SNaQ estimation (from a 2023 workshop)
- the JuliaPhylo google group for common questions. Join the group to post/email your questions, or to receive information on new versions, bugs fixed, etc.
- search for answers in github issues and post a new issue to post a question or a report potential bugs.
For the SNaQ method in particular, 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
For the PhyloNetworks package, please cite:
- Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017). PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution 34(12):3292–3298. doi:10.1093/molbev/msx235
See CITATION.bib for the relevant reference(s).
Note
Much of this package was formerly part of PhyloNetworks v0.16.4 (and prior). PhyloNetworks v0.17, v1.0 and later have been stripped of functions implementing the SNaQ method.