Bug#587189: ITP: python-nast -- alignment of short DNA sequences
Package: wnpp
Severity: wishlist
Owner: Steffen Moeller <steffen_moeller@gmx.de>
* Package name : python-nast
Version : 1.1
* URL : http://pynast.sf.net
* License : GPL
Programming Lang: Python
Description : alignment of short DNA sequences
The package provices a reimplementation of the Nearest Alignment
Space Termination tool in python. It was prepared for next generation
sequencers.
.
Given a set of sequences and a template alignment, PyNAST will align the
input sequences against the template alignment, and return a multiple
sequence alignment which contains the same number of positions (or
columns) as the template alignment. This facilitates the analysis of new
sequences in the context of existing alignments, and additional data
derived from existing alignments such as phylogenetic trees. Because
any protein or nucleic acid sequences and template alignments can be
provided, PyNAST is not limited to the analysis of 16s rDNA sequences.
.
Since version 1.1, PyNAST no longer exactly matches the output
of the origianl NAST program. Instead it focuses on getting better
alignments. Users who wish to exactly match the results of NAST should
download PyNAST 1.0.
.
PyNAST: a flexible tool for aligning sequences to a template
alignment. J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman,
Todd Z. DeSantis, Gary L. Andersen, and Rob Knight. January 15, 2010,
DOI 10.1093/bioinformatics/btp636. Bioinformatics 26: 266-267.
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