Metadata-Version: 2.1
Name: dnds
Version: 2.1
Summary: Calculate dN/dS ratio precisely (Ka/Ks) using a codon-by-codon counting method.
Home-page: https://github.com/adelq/dnds
Author: Adel Qalieh
Author-email: adelq@med.umich.edu
License: MIT
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics

dN/dS Calculator
================

.. image:: https://travis-ci.org/adelq/dnds.svg?branch=master
   :target: https://travis-ci.org/adelq/dnds

.. image:: https://img.shields.io/pypi/v/dnds.svg?maxAge=2592000?style=plastic
    :target: https://pypi.python.org/pypi/dnds

Calculate dN/dS ratio precisely (Ka/Ks) using a codon-by-codon counting
method. Also calculates the pN/pS ratio precisely (previously referred to as
dN/dS).

Usage
-----

.. code:: python

    >>> sequence_1 = "ATGCTTTTGAAATCG"
    >>> sequence_2 = "ATGCGTTCGAAGTCG"
    >>> pnps(sequence_1, sequence2)
    Fraction(38, 71)
    >>> round(float(pnps(sequence_1, sequence2)), 3)
    0.535
    >>> round(dnds(sequence_1, sequence_2), 3)
    0.467


