LASTZ is a tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. It is a drop-in replacement for BLASTZ, and is backward compatible with BLASTZ's command-line syntax.
LASTZ is designed to preprocess one sequence or set of sequences (which we collectively call the target) and then align several query sequences to it. The general flow of the program is like a pipeline: the output of one stage is the input to the next. The user can choose to skip most stages via command-line options; any stages that are skipped pass their input along to the next stage unchanged. Two of the stages, scoring inference and interpolation, are special in that they perform a miniature version of the pipeline within them.
Examples are available in /usr/local/apps/LASTZ/test_data/.
LASTZ uses environment modules. Type
module load LASTZ
then type lastz at the prompt: