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Calculate dn ds ratio for the whole tree with python

Hello, I'm using the codeml application with the python package ete3 in order to calculate the dN/dS ratio of my trees, but it appears that there is no possibility to calculate a such ratio for all the three, only for the branches.

Does someone know why ? And if so if there are other package in order to calculate a global dN/dS for the whole tree?

Thank you for your help.

Here Is an exemple where I succeed with ete3 to calculate the dN/dS ratio (in red) for all branches: enter image description here But what I would like is to get a global dN/dS for all the tree (the cluster) and not just for each branche .

python codeml ete3
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written by Darrill • Darrill

What do you mean by "all the tree"? What is there if not the branches?

Could you show some example data?

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written by Joe Joe

Hello, I updated my post.

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written by Darrill • Darrill

What is the overall objective?

I’m no expert but I’m not sure a dNdS for the whole tree/clade is particularly meaningful...I stand to be corrected.

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written by Joe Joe

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