lagan

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.