conk

Cython Smith-Waterman aligner for C3POa

Requirements:

Cython
setuptools
wheel

These packages should be pip installed:

python3 -m pip install --user --upgrade Cython setuptools wheel

To build the module and install, run make. To clean up this directory, run make clean.

Usage in python:

from conk import conk

seq = 'AAAAA'
penalty = 20

scores = conk.conk(seq, seq, penalty)