ssw-py: Striped Smith-Waterman SIMD accelerated Python Package for Use in Genomic Applications
This library uses the excellent source code from this is original source repository
Please cite this PLOS ONE paper by Zhao et al. 2013 when using this software.
Overview
ssw-py provides 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.
Using ssw.AlignmentMgr, you can compute 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 Striped Smith-Waterman opens a gap, the gap open penalty alone is applied.
Installation
from PyPi
$ pip install ssw-py
or from source
$ python setup.py install
Documentation
See documentation for help on using these bindings.
1 maintainer
Metadata
1 maintainer
Release files for ssw-py 1.0.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| ssw-py-1.0.1.tar.gz | 111.6 kB | Details |
Built distributions (wheels)
Total release size: 3.2 MB
Release files / ssw-py-1.0.1.tar.gz
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Release files / ssw_py-1.0.1-cp311-cp311-win_amd64.whl
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Release files / ssw_py-1.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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Release files / ssw_py-1.0.1-cp310-cp310-win_amd64.whl
| Download URL | ssw_py-1.0.1-cp310-cp310-win_amd64.whl |
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