https://github.com/adelq/dnds

Calculate dN/dS ratio precisely (Ka/Ks) using a codon-by-codon counting method.
https://github.com/adelq/dnds

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Calculate dN/dS ratio precisely (Ka/Ks) using a codon-by-codon counting method.

• Host: GitHub
• URL: https://github.com/adelq/dnds
• Owner: adelq
• License: mit
• Created: 2016-05-11T15:23:34.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2018-04-30T15:50:10.000Z (over 6 years ago)
• Last Synced: 2024-10-29T20:57:23.170Z (17 days ago)
• Language: Python
• Size: 14.6 KB
• Stars: 25
• Watchers: 2
• Forks: 9
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

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README

        
dN/dS Calculator

================

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   :target: https://travis-ci.org/adelq/dnds

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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