(For the older version of Sigma, go here.
The significant change in this version of Sigma is the incorporation of an evolutionary model for scoring, as described in an accompanying manuscript (G. Jayaraman and R. Siddharthan, unpublished). See the NOTES file in the source distribution, or run the program without options, for a summary of changes. See the page for the previous version for more information.
Source code: here (March 22, 2010; tested on Linux only)