A stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints. Stepwise MaxChi and Phylpro methods have been implemented in the C programming language as well as in R. For details, see the paper by Graham, McNeney and Seillier-Moiseiwitsch.
The stepwise R package is available on the Comprehensive R Archive Network website under "contributed packages". You will have to have R installed on your system to use it. To install stepwise you can execute the following command in R:
Windows users can also install the package via the "Packages" menu item.