GitHub - johannjc/py3-swalign: Python3 cythonized smith-waterson local aligner

johannjc / py3-swalign Public

forked from detrout/py3-swalign

Notifications You must be signed in to change notification settings
Fork 0
Star 0

Python3 cythonized smith-waterson local aligner

Notifications

Name		Name	Last commit message	Last commit date
Latest commit History 13 Commits
swalign		swalign
.gitignore		.gitignore
README.rst		README.rst
blosum50.txt		blosum50.txt
dna.txt		dna.txt
setup.py		setup.py
test.py		test.py

Repository files navigation

SWAlign
-------

Yet another smith waterson alignment code.

I copied the algorithm from: http://www.codesofmylife.com/2011/05/13/smith-waterman-algorithm-for-local-alignment-in-python/

And then tried to make it faster. 

At least on my laptop I was able to do about 300, ~160 bp alignments per second.

Oh yes, it also only works correctly on python3.


-------
This fork returns the maxScore as well - and fixed an issue with the setup.py to include the numpy include dirs