MISAT is a program for estimating the likelihood surface for q (4 times the effective population size times the mutation rate) for microsatellite data. Two models are implemented: a stepwise mutation model and a mutation model allowing multi-step mutations, i.e. mutational jumps larger than on repeat unit in size. There are several other programs available for doing this type of analysis, and to my knowledge, this is probably the slowest program publicly distributed. It is, by now, somewhat outdated although the multi-step mutational model probably is not implemented in any other programs. For more information, please see Nielsen, R. 1997. A Maximum Likelihood Approach to Population Samples of Microsatellite alleles. Genetics. 146: 711-716, Nielsen R. 1997. A likelihood approach to populations samples of microsatellite alleles (vol 146, pg 711, 1997; see correction in Genetics 1997 147: 349a). and Nielsen, R. and P. J. Palsboll. 1999. Tests of Microsatellite Evolution: Multi-Step Mutations and Constraints on Allele Size. Mol. Phyl. Evol. 11: 477-484.
At the moment I only distribute a Windows executable version of the program. Please send enquiries regarding source code or executables for other platforms to me.