BLASTZ is Obsolete
BLASTZ has been replaced by LASTZ.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
- BLASTZ chaining had a problem that caused it to discard very
- 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.