Two OS-independent packages for R, currently in ongoing development on r-forge.

paleoPhylo: biodiversity analyses in a palaeontological and phylogenetic context

paleoPhylo contains functions to analyse how speciation, extinction & character change contribute to biodiversity and display these relationships graphically. The functions are designed to inform realistic models of clade evolution; examples are drawn from data on planktonic foraminifera or generated randomly.

splits: SPecies’ Limits by Threshold Statistics

splits contains tools for delimiting species and automated taxonomy at many levels of biological organization (eg. DNA barcoding, morphometrics), top-down (merging phylogenetic and phylogeographic methods) and bottom-up (single samples into >1 groups).