CHAOS: CHAins Of Scores

NEW: A journal publication describing CHAOS and its use in anchoring DIALIGN has appeared in BMC-Bioinformatics

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.