pyssw: python wrapper for Smith-Waterman Python Module

The C code for SWW alignment is derived from: original source repository

Please cite this PLOS ONE paper by Zhao et al. 2013

Overview

SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.

Note: When SSW open a gap, the gap open penalty alone is applied.

Installation

from PyPi

pip install pyssw

or from source

git clone  https://github.com/Runsheng/pyssw.git
cd pyssw
pip install .