FASTA version 33t04 is now available from:
This version corrects a serious (but very rare) bug that was
introduced with version 3.3, which could cause very good matches to be
missed when searching with query sequences with 'n's (DNA) or 'x's
In addition, this version provides an MPI (Message Passing Interface)
implementation of the PVM library vs library parallel comparison
programs. Thus, in addition to pv3compfa, pv3compfx, pv3comptfx, etc,
there are now mp3compfa, mp3compfx, etc. The MPI and PVM programs
share exactly the same source code files, so you must do an "rm *.o"
before making one version or the other. To make the MPI versions, use
I find the PVM version more flexible, because it allows you to specify
the number of jobs to schedule on multiprocessor machines and to
encode the relative speed of machines in the host configuration file.
MPI seems much less flexible, but MPI seems to be the parallel
environment more commonly supported by computer manufacturers. We do
not see any difference in the performance of the two systems.
Improvements in error reporting have been incorporated.
Windows and Mac versions should be available by the end of the month.