SNaQ

SNaQ is a Julia package as a part of the JuliaPhylo software ecosystem. The package implements the SNaQ method by Solís-Lemus & Ané (2016) to estimate a phylogenetic network from quartet concordance factors. See the PhyloNetworks package, which SNaQ depends on, for background on phylogenetic networks and for how to get help.

Join the PhyloNetworks google group for updates here.

More information about the pre-processing steps to get the input data for SNaQ can be found in PhyloUtilities and the snaq tutorial.

References

For the SNaQ network inference method itself:

• Claudia Solís-Lemus and Cécile Ané (2016). Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting. PLoS Genetics 12(3):e1005896. doi:10.1371/journal.pgen.1005896

For PhyloNetworks package:

• 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 the references in bibtex format.

Manual

• Installation
• • Install Julia
  • Install SNaQ
  • Test example
• Network estimation
• • Inputs for SNaQ
  • • Concordance factors
    • Starting tree
  • Estimating a network
  • • Choosing the number of hybridizations (hmax)
    • Suggestions and best practices
• Candidate networks
• • Optimizing parameters for a given network
  • Network score with no optimization
  • Candidate networks compatible with a known outgroup
• Quartet test for goodness of fit
• Visualizing observed and expected CFs
• Bootstrap
• • Running a bootstrap analysis
  • Support for tree and hybrid edges
• Improving runtimes
• • Parallel runs
  • Parallel quartet likelihood
  • Quartet subsampling
  • • Removing uninformative quartets
• Multiple alleles per species
• • Between-species 4-taxon sets
  • Within-species 4-taxon sets
• SNaQ error reporting

Library

For help on individual functions, see the library:

• Internal Documentation
• Public Documentation