Lagan Tookit are tools for genomic alignment. These include the MLAGAN multiple alignment tool, and Shuffle-LAGAN for alignment with rearrangements.. All three are based on the CHAOS local alignment tool and combine speed (regions up to several megabases can be aligned in minutes) with high accuracy.
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Michael Brudno, Chuong Do, Gregory Cooper, Michael F. Kim, Eugene Davydov, Eric D. Green, Arend Sidow and Serafim Batzoglou
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA,
Genome Research 2003 Apr;13(4):721-31.
Michael Brudno, Sanket Malde, Alexander Poliakov, Chuong Do, Olivier Courone, Inna Dubchak, and Serafim Batzoglou
Glocal alignment: finding rearrangements during alignment.
Bioinformatics. 2003;19 Suppl 1:i54-62.
Michael Brudno, Michael Chapman, Berthold Gottgens, Serafim Batzoglou, and Burkhard Morgenstern
Fast and sensitive multiple alignment of large genomic sequences
BMC Bioinformatics, 4:66 2003.