Biodiversity analysis with R (BIO-R)

Biodiversity analysis with R (BIO-R) is a set of R programs that do biodiversity analysis of molecular data, in order to calculate heterozygosity, diversity among and within groups, shannon index, number of effective allele, percent of polymorphic loci, Rogers distance, Nei distance, cluster analysis and multidimensional scaling 2D plot and 3D plot

You can include external groups for colored dendogram or MDS plots, and additionally obtain a Core Subset using molecular data and also phenotypic, geographical and any source of data.