The LAGAN Toolkit consists of four components: 

 CHAOS, a pairwise local aligner optimized for non-coding, and other
 poorly conserved regions of the genome.
 
 LAGAN, a highly parametrizable pairwise global alignment using local
 alignments generated by CHAOS as anchors.
 
 Multi-LAGAN, a progressive pairwise algorithm to produce multiple
 sequence alignments.
 
 Shuffle-LAGAN, a novel glocal algorithm that is able to find
 rearrangements in a global alignment.

Fast and sensitive multiple alignment of long genomic sequences. BMC
Bioinformatics 2003 4:66.

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple
alignment of genomic DNA. Genome Res 2003 13(4): 721-31.

Glocal alignment: finding rearrangements during alignment. Proceedings
of the ISMB 2003, Bioinformatics 19: 54i-62i.

WWW: http://lagan.stanford.edu/lagan_web/