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Bioinformatics. 2010 Jan 15;26(2):266-7. doi: 10.1093/bioinformatics/btp636. Epub 2009 Nov 13.

PyNAST: a flexible tool for aligning sequences to a template alignment.

Author information

  • 1Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.

Abstract

MOTIVATION:

The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API).

RESULTS:

The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis.

AVAILABILITY:

PyNAST is available at http://pynast.sourceforge.net.

PMID:
19914921
PMCID:
PMC2804299
DOI:
10.1093/bioinformatics/btp636
[PubMed - indexed for MEDLINE]
Free PMC Article
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