SiteSifter is a command-line application written in C#. It was developed on Windows, but may work in other operating systems with a .NET framework implementation. If you manage to get SiteSifter working with Mono (it may even work out of the box), please let me know!

You can download the source for SiteSifter here. It is provided as a Visual Studio 2008 project, but the .cs files should work as is in other environments.

SiteSifter requires multiple alignment files from the UCSC Genome Browser for its analysis, in addition to a corresponding annotation file listing the locations of genes in the human frame. The published analysis (PNAS 2008) used the 17-genome multiple alignment located here and the gene annotation file located here. All files must be decompressed.

All questions related to the implementation should be directed toward Josh (see the contact page).