README

See http://baboon.math.berkeley.edu/amap/ for more information.

INSTALL
=======

To build the AMAP alignment code change to the 'align' directory and type:

	% make


This distribution includes the compiled AmapDisplay.jar file. 
In case you want to build the AmapDisplay from the source code, 
you'll need ant (http://ant.apache.org) installed.  
Once ant is installed change to the 'display' directory, and type:

	% ant all

USE
===
To run AMAP with the default options change to the 'align' directory and type:
	% amap <multi-fasta-file-name>

If no file name is provided the list of options are printed.

In order to use the AMAP Display run AMAP with the -gui option, and save the output to a file, 
then use the file as the input to AmapDisplay. For example, type:

	% align/amap -gui examples/BB12020.tfa > examples/BB12020.tfa.out
	% java -jar display/AmapDisplay.jar examples/BB12020.tfa.out 


LICENSE
=======

The various bits of AMAP code are distributed under the GPL.  Please see the license
in the license directory for details.