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Sliding Window Ka/Ks (Dn/Ds) Analysis Via Python?

I am working in Python and performing Ka/Ks (dN/dS) ratio analysis.

I would like to ask for any suggestions for how to go about performing "within gene" or "sliding window" Ka/Ks analysis, such that a Ka/Ks ratio can be given for positions along the gene sequence.

This MATLAB tutorial really sums up exactly what I need, but I am obliged by my boss to use Python.

Anticipated output example

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Extra info

  • I am using Python2.7 and often use Biopython
  • My users are likely to run the programs from Windows machines
evolution protein
• 8,515 views • link
written by a1ultima a1ultima

thank you very much for this gem @karl.schmid, but indeed we plan to use sliding windows more for visual understanding as the paper suggests

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written by a1ultima a1ultima

Hi, 5 years later I have the exact same problem...did you figure it out? Thanks in advance

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written by mariamcurbelo2061 • mariamcurbelo2061

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