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Information about Amap

AMAP
Developer:Ariel Schwartz (UC Berkeley), Lior Pachter (UC Berkeley)
Latest release:2.0
OS:UNIX, Linux, Mac
Genre: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.

Input/Output

This program accepts sequences in FASTA format.

The output format includes: FASTA format, Clustal.

References

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

External links

Software development is the translation of a user need or marketing goal into a software product.[1][2] Software development is sometimes understood to encompass the processes of software engineering combined with the research and goals of software marketing
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University of California, Berkeley is a public research university located in Berkeley, California, United States. Commonly referred to as UC Berkeley, Berkeley and Cal
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University of California, Berkeley is a public research university located in Berkeley, California, United States. Commonly referred to as UC Berkeley, Berkeley and Cal
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multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In general, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a
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In bioinformatics, FASTA format is a text-based format for representing either nucleic acid sequences or protein sequences, in which base pairs or protein residues are represented using single-letter codes.
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In bioinformatics, FASTA format is a text-based format for representing either nucleic acid sequences or protein sequences, in which base pairs or protein residues are represented using single-letter codes.
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Clustal is a widely used multiple sequence alignment computer program. The latest version is 1.83. There are two main variations:
  • ClustalW: command line interface
  • ClustalX: This version has a graphical user interface.

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