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Developer(s)Ariel Schwartz (UC Berkeley), Lior Pachter (UC Berkeley)
Stable release
Operating systemUNIX, Linux, Mac
TypeBioinformatics tool
LicenceOpen source
WebsiteAMAP download

AMAP is a multiple sequence alignment program based on sequence annealing.[1] 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.


  1. ^ S. Schwartz, A.; Pachter, L. (19 January 2007). "Multiple alignment by sequence annealing". Bioinformatics. 23 (2): e24–e29. doi:10.1093/bioinformatics/btl311.

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