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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.
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