MDIV is a program that will simultaneously estimate divergence times and migration rates between two populations under the infinite sites model and under a finite sites model (HKY). The program can be used to test if there is evidence for migration between two populations or evidence for shared recent common ancestry. In addition, you get maximum likelihood estimates of the demographic parameters. The program assumes that there is no recombination. The output of the program are integrated likelihood surfaces for the three parameters: q (two times the effective population size times the mutation rate), M (2 times the migration rate) and T (the divergence time divided by the effective population size. For more information regarding the program, please see Nielsen, R. and J. W. Wakeley. 2001. Distinguishing Migration from Isolation: an MCMC Approach. Genetics 158: 885-896. This version of the program is only applicable to a single locus and assumes equal population sizes in all populations. A program with enhanced features and better documentation is available from Jody Hey's web site.
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.