
 $Id: README 407 2010-10-13 20:29:01Z wrp $

July, 2008/updated October 13, 2010

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     

================================================================
October, 2010

This version of the FASTA programs is version 3.6.

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/fasta3x.me 	(unix -me nroff file which describes version 3.4 -
			 some programs are missing and options may be
			 incomplete.)
	doc/fasta3x.doc (text version of fast3x.me - see comments above)

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.

Documentation on the pvm3/mpi versions of the programs is available
in:
	doc/readme.pvm_3.4

This directory has been restructured to separate different types of
files.  The subdirectories are:

	bin/	(if present) - executable program binaries
	conf/	FASTLIBS files for configuring database locations
	data/	scoring matrices (blosum50.mat, etc)
	doc/	documentation files
	make/	Makefiles for compiling the programs
	misc/	perl scripts for reformatting raw scores for 'R'
	seq/	sample query sequences (*.aa, *.seq), and a sample
		library (prot_test.lseg)
	sql/	perl scripts for creating MySQL/PostgreSQL databases
		and SQL files for searching them.
	src/	'C' source code for FASTA programs
	test/	test scripts for the FASTA programs on Unix and Windows

Bill Pearson
wrp@virginia.edu
