3 packages on CRAN
Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences from multiple sequence alignments in FASTA format. The implementation includes improved defaults and plotting capabilities and unlike the original 'MATLAB' version removes singleton SNPs by default.
Bayesian reconstruction of disease outbreaks using epidemiological and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>.
Data structures and methods for manipulating output of genetic population structure clustering algorithms. 'starmie' can parse output from 'STRUCTURE' (see <https://pritchardlab.stanford.edu/structure.html> for details) or 'ADMIXTURE' (see <https://www.genetics.ucla.edu/software/admixture/> for details). 'starmie' performs model selection via information criterion, and provides functions for MCMC diagnostics, correcting label switching and visualisation of admixture coefficients.