MismatchHetMutRate is a series of programs to perform mismatch analyses allowing for heterogeneity of mutation rates. The authors are Laurent Excoffier, and Stephan Schneider.
The software can be directly downloaded here.
The software can be cited as: Schneider, S. and L. Excoffier (1999) Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites. Application to human mitochondrial DNA. Genetics 152: 1079-1089.