pyssw 0.1.7

Python wrapper for SSW alignment

# pyssw: python wrapper for Smith-Waterman Python Module

The C code for SWW alignment is derived from: [original source repository](https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library)

Please cite this [PLOS ONE paper](http://dx.plos.org/10.1371/journal.pone.0082138) 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](https://pypi.org/project/pyssw/)

pip install pyssw

or from source

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