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

Item Type Journal Article
Author J Gregory Caporaso
Author Kyle Bittinger
Author Frederic D Bushman
Author Todd Z Desantis
Author Gary L Andersen
Author Rob Knight
URL http://www.ncbi.nlm.nih.gov/pubmed/19914921
Publication Bioinformatics (Oxford, England)
ISSN 1367-4811
Date Nov 13, 2009
Extra PMID: 19914921
Journal Abbr Bioinformatics
DOI 10.1093/bioinformatics/btp636
Accessed 2009-12-30 14:29:00
Library Catalog NCBI PubMed
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. PyNAST is a complete re-implementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command line interface, and a simple API. RESULTS: The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to data sets 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. CONTACT: rob.knight@colorado.edu.
Title PyNAST: A flexible tool for aligning sequences to a template alignment
Short Title PyNAST
Date Added 2009-12-30 09:29
Date Modified 2009-12-30 09:29