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