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KaKs python 3 (li formula)

Hi everyone, i'm actually trying to creat a python script to get the divergence between two sequences. Then, i need to write a script with the kaKs calculation (function estimates the Ka and Ks values for a set two aligned sequences using the method published by Li (1993) and gives the associated variance matrix). So, I'm wondering if someone knows if there was a package available on python to do such a thing?

Thanks a lot and have a nice day!

sequence
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written by Chvatil Chvatil

It’s not a python package, but I believe PAUP can calculate this.

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written by Joe Joe

Well, R as well but i'm looking for a solution directly with python it is more powerfull :) Or if someone can give the formula with all the explanation I could code it directly I guess

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written by Chvatil Chvatil

1 answer

Please use the ADD REPLY found bellow the comment you want to address.

edit: the original paper (Li, 1993) describes the formulas in detail. According to a comment on Li paper, Pamilo & Bianchi (1993) arrives independently at the same method, this paper also describes the formulas in detail. If you want to implement the method yourself, I think these are good sources.

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written by h.mon h.mon

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