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

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.