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


BACKGROUND
PyNAST is available at http://pynast.sourceforge.net.
Caporaso
J Gregory
JG
Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.
Bittinger
Kyle
K
Bushman
Frederic D
FD
DeSantis
Todd Z
TZ
Andersen
Gary L
GL
Knight
Rob
R
D000465:Algorithms; D030541:Databases, Genetic; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software; D014584:User-Computer Interface