- The bpp-popgen library provides classes for population genetics analysis. It makes intensive use of the bpp-seq library, and adds a dedicated container named bpp::PolymorphismSequenceContainer, which associates frequencies to the sequences in the set. The bpp::PolymorphismSequenceContainerTools and bpp::SequenceStatistics static classes provide several tools for data analysis, including diversity indices and positive selection tests.
Population and sample data storage and manipulation
- PopGenLib library provides data structure for handling sample and data sets for population genetics. These objects are embedded in the bpp::DataSet object which is a container of bpp::Group of bpp::Individual. Each bpp::Individual can store bpp::Sequence data or allelic data with the dedicated classes bpp::MultilocusGenotype.
Population genetics data and statistics
- To compute statistics on data, two containers families are provided, one for sequences (bpp::PolymorphismSequenceContainer) and the other for allelic data (bpp::PolymorphismMultiGContainer). Static tools class for both families are provided to compute several common or less common statistics.
Statistics overview
- heterozygosity
- watterson75 Diversity estimator Theta of Watterson
- tajima83 Diversity estimator Theta of Tajima
- DVH Haplotype diversity of Depaulis and Veuille
- D Tajima's D test