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Developer(s) Ariel Schwartz (UC Berkeley), Lior Pachter (UC Berkeley)
Stable release
Operating system UNIX, Linux, Mac
Type Bioinformatics tool
Licence Open source
Website AMAP download

AMAP is a multiple sequence alignment program based on a new approach to multiple alignment called sequence annealing. This approach consists of building up the multiple alignment one match at a time, thereby circumventing many of the problems of progressive alignment. The AMAP parameters can be used to tune the sensivitiy-specificity tradeoff.

The program can be used through the AMAP web server or as a standalone program which can be installed with the source code.


This program accepts sequences in FASTA format.

The output format includes: FASTA format, Clustal.


A. Schwartz and L. Pachter, Multiple alignment by sequence annealing, Bioinformatics 23, e24-e29 (2006).

External links[edit]