Below is an alphabetical list of the algorithms created so far from each CNS CIShell-powered tools. Some pages are still fairly rough but most are pretty good :)
If you would like to view an index of algorithms in a particular CNS CIShell-powered tool, see the Sci2 Algorithm Index, the NWB Manual, or the EpiC Manual.
Source code for these algorithms is browsable in the CNS Center repository, see Document & Developer Resources (direct link to repository is currently down. Should be available soon as of March 2011).