Protein multiple alignment by sequence annealing

 AMAP is a command line tool to perform multiple alignment of peptidic
 sequences. It utilizes posterior decoding, and a sequence-annealing
 alignment, instead of the traditional progressive alignment method. It is
 the only alignment program that allows one to control the sensitivity /
 specificity tradeoff. It is based on the ProbCons source code, but
 uses alignment metric accuracy and eliminates the consistency
 transformation.
 .
 The java visualisation tool of AMAP 2.2 is not yet packaged in Debian.