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omegaMap is a program for detecting natural selection and recombination in DNA or RNA sequences. It is based on a model of population genetics and molecular evolution. The signature of natural selection is detected using the dN/dS ratio (which measures the relative excess of non-synonymous to synonymous polymorphism) and the signature of recombination is detected from the patterns of linkage disequilibrium. The model and the method of estimation are described in

Wilson, D. J. and G. McVean (2006)
Estimating diversifying selection and functional constraint in the presence of recombination.
Genetics doi:10.1534/genetics.105.044917. (abstract pdf)

From here you can download the documentation, ready-to-use executables and source code.