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

• DOI: 10.1093/bioinformatics/btp636
• Publication Date: 2009-11-14T01:25:01Z
• Authors: J. Gregory Caporaso; Kyle Bittinger; Frederic D. Bushman; Todd Z. DeSantis; Gary L. Andersen; Rob Knight
• Keywords: Software portability; Python; Interface (matter); Graphical user interface; Application programming interface; Feature (linguistics)

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 original implementation, it has not been as widely adopted possible. Python (PyNAST) a complete reimplementation NAST, which includes three convenient interfaces: Mac OS X GUI, command-line interface and simple application programming (API). Results: availability PyNAST will make popular NAST algorithm more portable thereby applicable datasets orders magnitude larger by allowing users install on their own hardware. Additionally because can align arbitrary template alignments, feature available via web interface, be readily novel tasks outside analysis. Availability: at http://pynast.sourceforge.net. Contact: [e-mail]