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IM is a program, written with Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations. IM is based on a method originally developed by Rasmus Nielsen and John Wakeley (Nielsen and Wakeley 2001 Genetics 158:885). Large numbers of loci can be studied simultaneously, and different mutation models can be used.

IMa implements the same Isolation with Migration model, but does so using a new method that provides estimates of the joint posterior probability density of the model parameters. IMa also allows log likelihood ratio tests of nested demographic models. IMa is based on a method described in Hey and Nielsen (2007 PNAS 104:2785–2790). IMa is faster and better than IM (i.e. by virtue of providing access to the joint posterior density function), and it can be used for most (but not all) of the situations and options that IM can be used for.

Required Modules


  • ima

System Variables



If you publish research that uses ima you have to cite it as follows:

Nielsen, R, and J Wakeley. 2001. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158(2): 885-896 Abstract

Hey, J, and R Nielsen. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. PNAS 104(8):2785-90. Abstract


  • Validated 4/5/2018