BLASTZ is Obsolete

BLASTZ has been replaced by LASTZ. Researchers who are familiar with BLASTZ can depend on the fact that LASTZ is backward compatible, in the sense that it will recognize all of the same command line options that BLASTZ provided. The only alignment differences they should encounter are the result of bug fixes, such as:

• BLASTZ had a "short-by-two" error. In many cases, it shortened alignments by two bases on either or both ends.

• BLASTZ had a problem with premature alignment termination.

• BLASTZ used the ydrop value from the main alignment as the xdrop value for interpolation.

• BLASTZ had a problem when ydrop is less than the penalty for a one-base gap.

• BLASTZ chaining had a problem that caused it to discard very high-scoring HSPs.

• The handling of ties in the DP matrix was unspecified in BLASTZ. This has changed in LASTZ, which specifically prefers a longer alignment to a shorter alignment with the same score. This change reflects the use of LASTZ to align short reads, and desire to align as much of the read as possible.

• The default handling of bounding alignments in the DP matrix is different in LASTZ than in BLASTZ. The option ‑‑allgappedbounds can be used to revert to the bounding criteria used in BLASTZ.

For more information about these fixes and the many additional features available in LASTZ, please see the LASTZ documentation.