
 $Id: README 634 2011-03-25 13:11:26Z wrp $

March, 2011

This version of the FASTA programs is fasta-36.3.4.  With this
version, 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.

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/	some perl scripts
      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/fasta35_t, etc.)

For a simple test of a program, try (from the src directory)

   ../bin/fasta35 -q ../seq/mgstm1.aa ../seq/prot_test.lseg     

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

Bill Pearson
wrp@virginia.edu
