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Lastz
<A href=http://www.bx.psu.edu/~rsharris/lastz>Lastz</A>, developed by <A href=http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdfR. S. Harris as part of his PhD research</A>, is a tool for comparing two large genomes.
http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html#intro
