Amap, Multiple Alignment by Sequence Annealing, had been developed by Ariel Schwartz at UC Berkeley. It implements novel algorithms to improve the computation of multiple sequence alignments. Java and BioJava-programmers can now take advantage of Amap using the STRAP-toolbox API. Please visit the section SequenceAligner in http://3d-alignment.eu/Scripting.html. Amap is also available for users of the STRAP-workbench http://3d-alignment.eu/.
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