A new version of the FASTA3 package of programs - fasta32t01.shar.Z -
is available from ftp://ftp.virginia.edu/pub/fasta.
This version has three major improvements:
(1) DNA sequences are now searched in both orientations by default by
fasta3 and fastx/y3; as a result, the program is 1/2 as fast, but
and additional run is not required. The '-1' option reverts to the
old single orientation mode.
(2) DNA alignment numbering is now much more sensible. In particular,
reverse complement alignments count backwards, and DNA-protein alignments
use DNA coordinates for the DNA strand, even if a translated protein
alignment is shown.
(3) There is a new program, fasts3(_t), which searches for unordered
peptide fragments - reordering the fragments to find the best
Mac and PC versions will be available in a few weeks.
As always, keep those bug reports coming.