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

James G Caporaso; Kyle Bittinger; Frederic D. Bushman; Todd Z. Desantis; Gary L. Andersen; Rob Knight

doi:10.1093/bioinformatics/btp636

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

James G Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. Desantis, Gary L. Andersen, Rob Knight

Research output: Contribution to journal › Article

2113 Scopus citations

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.

Original language	English (US)
Article number	btp636
Pages (from-to)	266-267
Number of pages	2
Journal	Bioinformatics
Volume	26
Issue number	2
DOIs	https://doi.org/10.1093/bioinformatics/btp636
State	Published - 2010
Externally published	Yes

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ASJC Scopus subject areas

Biochemistry
Molecular Biology
Computational Theory and Mathematics
Computer Science Applications
Computational Mathematics
Statistics and Probability

Cite this

Caporaso, J. G., Bittinger, K., Bushman, F. D., Desantis, T. Z., Andersen, G. L., & Knight, R. (2010). PyNAST: A flexible tool for aligning sequences to a template alignment. Bioinformatics, 26(2), 266-267. [btp636]. https://doi.org/10.1093/bioinformatics/btp636

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10.1093/bioinformatics/btp636