
                          AMAP 2.01
                          ~~~~~~~~~                          

   A fast and accurate multiple sequence alignment program

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AMAP is a novel algorithm for producing multiple sequence alignments. 
It utilizes posterior decoding, and a novel sequence-annealing alignment, 
instead of the traditional progressive alignment method.
It is the only alignment program that allows to control the sensitivity / specificity tradeoff.
In its default configuration, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score - 
a new alignment accuracy measure, based on a metric for the multiple-alignment space, 
which integrates sensitivity and specificity into a single balanced measure.

AMA is defined as the fraction of correctly aligned residues (either to another residue or to a gap) out of
the total number of residues in all the sequences.

For more details on AMAP and AMA, see

   Schwartz, Ariel S., Myers, Eugene W., and Pachter, Lior.
   Alignment Metric Accuracy (Submitted for publication).

and for more details on sequence-annealing, see

   Schwartz, Ariel S. and Pachter, Lior.
   Multiple Alignment by Sequence Annealing. 
   in the Proceedings of the European Conference on Computation Biology (ECCB), 
   Eilat, Israel, September 2006.

The current version of AMAP uses the PROBCONS 1.09 code base for some of the input/output procedures,
and for the calculation of posterior probabilities (see PROBCONS.README). Future releases might implement
the algorithm using a new independent code base.

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AMAP has been made  freely  available as PUBLIC DOMAIN
software and hence is not subject to copyright in the United
States. This system and/or any portion of the source code
may be used, modified, or redistributed without restrictions.  
AMAP is distributed WITHOUT WARRANTY, express or implied.
The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for
loss due to reliance on the program.
   
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Version History

AMAP.1.0, 8/15/2005 (Ariel Schwartz)
   -- initial release
AMAP.1.1, 2/20/2006 (Ariel Schwartz)
   -- Fixed a bug with the calculation of gap posterior probabilities of multiple-sequence-alignments (no effect on pairwise alignments).
AMAP.2.0  4/16/2006 (Ariel Schwartz)
   -- Implemented the sequence-annealing alignment methods as an improved alternative to progressive alignment.
AMAP.2.01 6/8/2006  (Ariel Schwartz)
   -- Corrected DNA alignment parameters file. Improved debug output.
AMAP.2.1  7/21/2007 (Ariel Schwartz)
   -- Includes new output for the AMAP Display Java based GUI