NEW: CHAOS is now distributed as part of the LAGAN package, available here.
CHAOS is a heuristic local alignment tool developed by Michael Brudno of Stanford
University's Computer Science Dept in a collaboration with Burkhard
Morgenstern. It has been used for anchoring the
DIALIGN and
LAGAN global alignment programs.
An abstract describing the motivation for
CHAOS and the algorithms used in it was presented as a poster
presentation for RECOMB
2002
A full paper describing the
algorithm and some applications appears in the Proceedings of the IEEE Computer Society
Conference on Bioinformatics p. 138
A tarball of the CHAOS source can be downloaded. This is the corresponding README. If you use CHAOS, please consider subscribing to the LAGAN mailing list, so that I can keep you updated of the latest improvements and bugfixes.