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

TLDR

NAST is widely used in microbial ecology but its limited portability has restricted broader adoption. PyNAST reimplements NAST in Python to broaden accessibility. PyNAST is implemented in Python and offers a Mac OS X GUI, command‑line, and API for alignment. PyNAST enhances portability, enabling use on larger datasets and allowing alignment to arbitrary template alignments, expanding its applicability beyond microbial community analysis. PyNAST is available at http://pynast.sourceforge.net and can be contacted at [e-mail].

Abstract

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. Availability: PyNAST is available at http://pynast.sourceforge.net. Contact: [e-mail]