A new version of the fasta distribution, fasta34t25d5.shar.Z, is
In general, the major changes in this version are internal; the
functions producing alignments and alignment coordinates have been
simplified. One of the consequences is that for the parallel
versions, alignments are calculated only once, even if the alignment
information is needed several times (e.g. in the list of best scores
and as final alignments).
The major new feature is the ability to work with asymmetric scoring matrices.
Although the FASTA programs use the NxN scoring matrix format used by BLAST,
only half of the matrix was actually read andthe rest inferred by symmetry.
This has been changed, and asymmetric matrices can be used.
In addition, the -V "*#" annotation option is now available in the
parallel versions of the programs, and some minor bug fixes are