Garza and Williamson (2001) demonstrate how M, the ratio of the number of alleles to range in allele size, for a sample of microsatellite loci can be used to detect reductions in effective population size. Two simple software programs related to this ratio are available for download here.
M_P_Val.exe calculates the value of M for a microsatellite data set. It will then simulate an equilibrium distribution of M, according to the method described in Garza and Williamson (2001), and given assumed values for the three parameters of the two-phase mutation model, and rank the calculated value relative to the equilibrium distribution. Using conventional criteria, there is evidence of a significant reduction in population size if less than 5% of the replicates are below the observed value. The input file consists of the relative allele sizes, simple allele counts and assumed mean values for the three parameters: theta=4*effective population size*mutation rate, ps=mean percentage of mutations that add or delete only one repeat unit (the program actually uses ps-1) and deltag=mean size of larger mutations. The proper format for the input file is described here. In a survey of empirical mutation data from the literature, Garza and Williamson (2001) found ps=0.88 and deltag=2.8. Theta will be population specific.
Download M_P_Val.exe here
Download M_P_Val for Mac OSX here
Critical_M.exe will take the number of individuals sampled, the number of loci for which there is data and the three assumed parameter values for the two-phase mutation model and calculate a critical value, Mc, through simulation as decribed in Garza and Williamson (2001). Ten thousand simulation replicates are performed and the M ratio is calculated for each. These values are ranked and Mc is defined such that only 5% of the simulation values fall below.
Download Critical_M.exe here
Download Critical_M for Mac OSX here
Note: These run only on Mac OS. The OSX versions are self-extracting. M_P_Val for OSX has a GUI. Critical_M for OSX runs on the command line (Terminal.app). For instructions on how to run it, go here.
An extensive list of software for population genetic analysis, focusing mainly on phylogeny programs, can be found here .