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

Bioinformatics
J Gregory CaporasoRob Knight

Abstract

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

Associated Clinical Trials

Jan 16, 2015·Craig A. Friesen, MD

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Citations

Jul 16, 2013·Veterinary Microbiology·Darin C BennettKimberly M Cheng
Jun 4, 2010·The ISME Journal·Elizabeth K CostelloRob Knight
Sep 29, 2012·The ISME Journal·Patrick D Schloss
Jul 27, 2012·The ISME Journal·J Kirk HarrisNorman R Pace
Apr 5, 2013·The ISME Journal·Christian L LauberNoah Fierer
Dec 4, 2012·Nature Methods·Nicholas A BokulichJ Gregory Caporaso
Mar 4, 2011·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey J WernerLargus T Angenent
May 5, 2012·Bioinformatics·Elmar PruesseFrank Oliver Glöckner
Mar 21, 2013·Bioinformatics·David WeismanJennifer L Bowen
Jan 10, 2013·The Journal of Infectious Diseases·Henry RedelMartin J Blaser
Aug 26, 2010·Genome Research·Chaysavanh ManichanhFrancisco Guarner
Sep 7, 2013·Science·Vanessa K RidauraJeffrey I Gordon
Apr 2, 2013·Applied and Environmental Microbiology·S BougouffaP Y Qian
Aug 9, 2011·Applied and Environmental Microbiology·Toru TakeshitaYoshihisa Yamashita
Jun 25, 2013·Applied and Environmental Microbiology·Nicholas A Bokulich, David A Mills
Jul 23, 2013·Applied and Environmental Microbiology·Kelly L RoeKatherine A Barbeau
Sep 4, 2012·Applied and Environmental Microbiology·Danilo ErcoliniMichele Iacono
Nov 6, 2012·Applied and Environmental Microbiology·Stefanie KautzCorrie S Moreau
Aug 2, 2011·Applied and Environmental Microbiology·Robert M BowersNoah Fierer
Jun 7, 2013·Journal of Clinical Microbiology·Nicholas A BokulichMark A Underwood
Oct 31, 2013·MBio·Elizabeth K CostelloDavid A Relman
Jan 14, 2012·American Journal of Physiology. Gastrointestinal and Liver Physiology·Ece A MutluAli Keshavarzian
Nov 16, 2012·American Journal of Physiology. Regulatory, Integrative and Comparative Physiology·Hannah V CareyRob Knight
Jun 18, 2011·American Journal of Respiratory and Critical Care Medicine·Emily S CharlsonRonald G Collman
Aug 24, 2013·BMC Gastroenterology·Neelendu DeySteven E Brenner
Nov 8, 2012·PLoS Computational Biology·Steven W KembelJessica L Green
Dec 29, 2010·PloS One·Emily S CharlsonRonald G Collman
Dec 2, 2011·PloS One·Gilberto E FloresNoah Fierer
Jun 2, 2012·PloS One·Guoyun BaiRebecca M Brotman

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Software Mentioned

NAST
PyNAST )
BLAST
Greengenes
MUSCLE
NumPy
PyCogent
PyNAST
Python
Nearest Alignment Space Termination ( NAST )

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