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LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.
To run this software interactively in a Linux environment run the commands:
module load lastz lastz file1.fa file2.fa [options]
where file1.fa and file2.fa are the 2 sequences being compared. For a complete listing of options, see the LASTZ documentation.