AMAP


AMAP

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 [http://baboon.math.berkeley.edu/mavid/ AMAP web server] or as a standalone program which can be installed with the [http://bio.math.berkeley.edu/amap/download/ source code] .

Input/Output

This program accepts sequences in FASTA format.

The output format includes: FASTA format, Clustal.

References

A. Schwartz and L. Pachter, [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/2/e24 Multiple alignment by sequence annealing] , Bioinformatics 23, e24-e29 (2006).

External links

* [http://baboon.math.berkeley.edu/mavid/ AMAP web server]


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