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
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
A full paper describing the algorithm and some applications appears in the Proceedings of the IEEE Computer Society Conference on Bioinformatics p. 138