Quarnet GoF –or simply QGoF
QuartetNetworkGoodnessFit.jl is a Julia package for phylogenetic networks analyses using four-taxon subsets. It includes tools to measure the goodness of fit of a candidate network to data on subsets of 4 tips. It depends on the PhyloNetworks package.
For a tutorial, see the manual:
- goodness of fit of a candidate network
- quartet concordance factor simulation
- expected concordance factors
References:
- Ruoyi Cai & Cécile Ané (2021). Assessing the fit of the multi-species network coalescent to multi-locus data. Bioinformatics, 37(5):634-641.
- Noah W. M. Stenz, Bret Larget, David A. Baum, and Cécile Ané (2015). Exploring tree-like and non-tree-like patterns using genome sequences: An example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh. Systematic Biology, 64(5):809-823.
- Addendum describing a modification to the model in the original TICR test.