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.
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Genetics. 2001 Jun;158(2):885-96.
Distinguishing migration from isolation: a Markov chain Monte Carlo approach.
Nielsen R, Wakeley J.