stepwise

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.

You may download the C source code and documentation for both procedures as a gzipped tar file, or as a zip file. The PDF documentation file is available here.

The stepwise R package is available on the Comprehensive R Archive Network website. You will have to have R installed on your system to use it. To install stepwise you can execute the following command in R:

install.packages("stepwise")

Windows users can also install the package via the "Packages" menu item.

The software is licenced under the GNU General Public Licence.