LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA

Michael Brudno, Chuong B. Do, Gregory M. Cooper, Michael F. Kim, Eugene Davydov, NISC Comparative Sequencing Program, Eric D. Green, Arend Sidow, and Serafim Batzoglou
Genome Research 13(4):721–731, Apr 2003
http://lagan.stanford.edu/mlagan_gr.pdf

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