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README
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README
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[This file has been replaced by README.md]
December, 2017
The most up-to-date version information on FASTA versions is available
in README.md and doc/readme.v36 .
July, 2015
This version of the FASTA programs is fasta-36.3.8. Since March, 2011
(fasta-36.3.4), the FASTA programs are no longer interactive. Typing
bin/fasta36 (or any of the other programs) provides a help message.
The "classic" interactive mode is available by typing "fasta36 -I".
In addition, there is only one version of the programs, "fasta36",
"ssearch36", etc., which is threaded by default on Unix/Linux/MacOSX.
As of November, 2014, the FASTA program code is avaiable under the
Apache 2.0 open source license.
Up to date release notes are available in the file doc/readme.v36
Documentation on the fasta3 version programs is available in the files:
doc/fasta36.1 (unix man page)
doc/changes_v36.html (short descriptions of enhancements to
FASTA programs)
doc/readme.v36 (text descriptions of bug fixes and version history)
doc/fasta_guide.tex (Latex file which describes fasta-36,
and provides an introduction to the FASTA programs,
their use and installation.)
doc/fasta_guide.pdf (printable/viewable description of fasta-36)
The latter two files provide background information on installing the
fasta programs (in particular, the FASTLIBS file), that new users of
the fasta3 package may find useful.
================================================================
The FASTA distribution directories (this directory) has been
substantially re-organized to make it easier to find things. However,
some documentation has not yet been completely updated to reflect the
re-organization, so some things may not make sense.
Files can now be found in several sub-directories
bin/ (pre-compiled binaries for some architectures)
conf/ example fastlibs files
data/ scoring matrices
doc/ documentation files
make/ make files
misc/ perl scripts to reformat -m 9 output, convert -R search.res files for 'R', and embed domains in shuffled sequences
scripts/ perl scripts for -V (annotate alignments) and -E (expand library) options
seq/ test sequences
src/ source code
sql/ sql files and scripts for using the sql database access
test/ test scripts
For some binary distributions, only the doc/, data/, seq/, and bin/,
directories are provided.
================
To make the standard FASTA programs:
cd src
make -f ../make/Makefile.linux_sse2 all
where "../make/Makefile.linux_sse2" is the appropriate file for your system.
The executable programs will then be found in ../bin
(e.g. ../bin/fasta36, etc.)
For a simple test of a program, try (from the src directory)
../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg
================================================================
Bill Pearson
wrp@virginia.edu