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[jabaws.git] / website / archive / binaries / mac / src / fasta34 / README.versions

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-
-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).
-