README.first for LAGAN Toolkit (Limited Area Global Alignment of Nucleotides) v2.0   
Author: Michael Brudno (brudno@cs.toronto.edu)                  09/14/2006

LAGAN was developed by 
Michael Brudno, Chuong Do, Sanket Malde, Michael F Kim and Serafim Batzoglou of 
the Dept of Computer Science at Stanford University, with assistance from many 
other people. See http://lagan.stanford.edu or contact lagan@cs.stanford.edu
for more information.

0. Availability + Legalese
   The source code of this version of LAGAN is freely available to all users 
under the GNU Public License (GPL). See the file LICENSE in this directory for more 
information. You can download the LAGAN sources from http://lagan.stanford.edu
If you use LAGAN regularly please consider contacting lagan@cs.stanford.edu 
to be placed on a mailing list to be contacted about any updates and bug-fixes. 
If you use LAGAN in a published result please see 
http://lagan.stanford.edu/cite.html for the latest citation information.

I. Installation 
   To install LAGAN you need to copy the source files to your local 
computer, untar/ungzip them, and run "make". I am assuming you have a 
reasonably modern installation of gcc and perl. The sequence of commands should 
be:

% gunzip lagan.tar.gz
% tar xvf lagan.tar
% make
 
This will create the executable files chaos, anchors, order, mlagan, 
glocal, prolagan as well as many tools in the utils directory. 

You may also need to go into all the .pl file, and change the first line
to call your perl interpreter.

Because LAGAN uses no system-dependent or implementation dependent 
libraries it should compile on all platforms and ANSI C compilers. 
We use it on a Linux box. Please tell us if you have trouble compiling/running 
LAGAN tools on your favorite platform, we have found that most of these problems 
are easily resolved.

II Description
LAGAN toolkit is a set of tools for local, global, and multiple alignment of DNA
sequences. Please see our website (http://lagan.stanford.edu) for publications 
describing LAGAN and its components.

The 4 main parts of LAGAN, each documented in its own README file are:

1. CHAOS local alignment tool
2. LAGAN pairwise global alignment tool
3. MLAGAN multiple global alignment tool.
4. Shuffle-LAGAN pairwise glocal alignment (with the SuperMap chaining addition)

There are also numerous utilities and scripts, mainly in the utils subdirectory.
Some of these are documented in the README.tools file. Of particular interest 
may be scorealign, that can score a LAGAN or MLAGAN alignment, and the series 
of "m" tools: mproject, mextract, mpretty, mrunfile for running mlagan and 
parsing its output.


III Repeat Masking

LAGAN, MLAGAN, and Shuffle-LAGAN can use masking information to improve 
the quality of the alignment. If you are trying to align sequence seq1.fa 
and seq2.fa you should create the files seq1.fa.masked and seq2.fa.masked 
which should have repeats masked to Ns. LAGAN, M-LAGAN and S-LAGAN 
will know to look for these files when aligning. CHAOS doesn't recognise 
repeat information, you should just use it on the masked files if this is 
appropriate.

IV Changes from previous version

0.9 -> 1.0: Several bug fixes, alignment parameters are now in the nucmatrix.txt file
1.0 -> 1.1: Several bug fixes, Fastreject now clips at intersection rather than union. 
1.1 -> 1.2: A few bug fixes, Shuffle-LAGAN added.
1.2 -> 1.21: A few bug fixes, sped up shuffle-lagan, code is now GPLed
1.21-> 2.0: A few minor (and couple of major) bug fixes. MLAGAN no longer 
requires a tree, and takes a substitution matrix as an argument, added 
supermap chaining (and a new implementation of glocal chaining), updated 
to align up to 63 sequences.