
Near Optimal Alignment Software    Version: rel-2-1
==============================================================================

This distribution includes a suite of software related to near optimal
sequence alignment.  The following packages are included:


noptalign (rel-2-1)
------------------------------------------------------------------------------
noptalign is a C++ program used to generate near optimal sequence alignments.
noptalign may be run independent of any of the other software.


noptdisplay (rel-2-1)
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noptdisplay is a Java application (and applet) that is used to visualize
near optimal sequence alignments.  noptdisplay requires noptalign 
(specifically, its output) to run.  


noptweb (rel-2-1)
------------------------------------------------------------------------------
noptweb is a Perl CGI web interface that coordinates the execution of
noptalign and noptdisplay. noptweb requires both noptalign and noptweb in
addition to various Perl packages.


Each package in this distribution contains its own installation instructions.
See the README files for simple instructions and the INSTALL files for more
details.  Brief instructions on unpacking and installing are provided below.



1. noptalign Installation
-------------------------

noptalign is a C++ program packaged with GNU autoconf.  Below is a listing of
the commands needed to install the software. For a more detailed description,
see the README and INSTALL files included in the respective packages.  

Install noptalign
	
	(in the directory where you downloaded the files)
	% tar -xvzf noptalign-rel-X-X.tar.gz
	% cd noptalign-rel-X-X
	% ./configure
	% make all check
	% sudo make install
	% cd ..

The noptalign application should now be usable.  Type:

	% noptalign

to give it a try.  Executing noptalign without any arguments should print
a USAGE statement.  See the README in the noptalign directory or the man
page for more details.


2. noptdisplay installation
---------------------------

The first step is to determine whether you want the binary only distribution 
(noptdisplay_bin_rel-X-X.tar.gz) or the source distribution 
(noptdisplay_src_rel-X-X.tar.gz).  If you only ever intend on running the 
software, then the binary distribution will be what you want.  
If you'd like to see the source code and possibly modify the software, 
then you will want the source distribution.  

The document will only describe the binary installation.  The README file
contained in the distribution will provide details for building the application
from source.

	(in the directory where you downloaded the files)
	% tar -xvzf noptdisplay_bin_rel-X-X.tar.gz
	% cd noptdisplay_bin_rel-X-X

Since noptdisplay is Java based, intallation is simply a matter of copying
all of the jar files found in the lib directory to your favorite location
for jars.  Alternatively, you can just leave everything where it is, and 
run the software from noptdisplay_bin_rel-X-X directory.

To run the software with a set of example alignments, do the following:

	(in the noptdisplay_bin_rel-X-X directory)
	% java -jar lib/noptdisplay.jar -a examples/sample_alignments 

See the README file that is part of the distribution for more details.


3. noptweb installation
-----------------------

The noptweb software provides a web interface to the noptalign and noptdisplay
software.  You should only need to use this software if you want to provide 
a local installation of http://fasta.bioch.virginia.edu/noptalign.  To 
install the software you will need some familarity with Apache and Perl.
Unpack the software as before:

	(in the directory where you downloaded the files)
	% tar -xvzf noptweb-rel-X-X.tar.gz

Then read the README file included with the distribution for details on 
how the software needs to be modified to run at your location and what 
other software must be installed.
