August, 2002

The latest versions of the FASTA search programs are in fasta3.shar.Z.
This file contains the fasta34 series of programs.  fasta34 also runs
the exact same functions threaded (fasta33, fasta33_t) and in parallel
using PVM and MPI.

Here is a list of the programs, and where they can be found:

program         fasta2          fasta34                 replaced by

fasta           yes             fasta34, fasta34_t

ssearch         yes             ssearch34, ssearch34_t

tfasta          yes             tfasta34, tfasta34_t    (tfastx34 preferred)

fastx           yes             fastx34, fastx34_t
fasty           no              fasty34, fasty34_t

tfastx          yes             tfastx34, tfastx34_t
tfasty          no              tfasty34, tfasty34_t

fasts/tfasts    no              fasts34(_t), tfasts34(_t)

fastf/tfastf    no              fastf34(_t), tfastf34(_t)

prss            yes             prss34

prfx            no              prfx34

================

The following programs are part of the fasta2 program package.  The
latest version of fasta2 is fasta20u66.shar.Z.

The most useful fasta2 programs are lalign and plalign, which calculate
multiple non-intersecting local alignments using Webb Miller's "sim"
implementation of the Waterman-Eggert algorithm.

You should not use the fasta2 programs for library searching; the
fasta3 programs are more sensitive and have better statistics.

lalign          yes             no

plalign         yes             no

flalign         yes             no

align           yes             no

align0          yes             no

lfasta          yes             no

randseq         yes             no

crandseq        yes             no

aacomp          yes             no

bestscor        yes             no

grease          yes             no

tgrease         yes             no

garnier         yes             no

================

The fasta3.shar.Z and fasta2.shar.Z files a Unix "shell archive" files.
To unpack them, go into an empty directory and type:

        zcat fasta3.shar.Z | sh

You can then make the programs by typing:

        make all

Makefile's are available for many platforms, e.g.

        make -f Makefile.linux
        make -f Makefile.sun

etc.  You are much better off using the pre-configured Makefile.???
than trying to edit the Makefile (which is designed for a Compaq/HP
Alpha).

Precompiled versions of the programs for Mac and Windows are available
in the mac_fasta and win32_fasta directories.  If you are running
MacOSX from the command line, use the Unix version (fasta3.shar.Z and
Makefile.os_x).