The BYPASSR and BYPASSRdegr software packages for estimating site-specific rates and degradation levels of ancient DNA sequences, respectively, are available from Ligia Mateiu’s web site
The MAPminer software for summarizing a posterior distribution of phylogenies is available from Karen Cranston’s website
Bayesian Phylogenetics and Phylogeography (BP&P)
The program BP&P (bpp2.1b.tgz) implements the Bayesian methods of Yang (2002), Rannala & Yang (2003), Burgess & Yang (2008), and Yang & Rannala (2010), for estimating population sizes (theta’s), species divergence times (tau’s), and for delimiting species using multi-locus sequence data from several closely related species. The mac OSX versions are here, for 32-bit (bpp2.1-mac-i386.tar.gz) and 64-bit (bpp2.1-mac-x86_64.tar.gz) intel chips.