How to specify a branch in the tree automatically for branch-site model codeml?
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6.9 years ago
sckinta ▴ 720

Hi I am trying to use codeml to evaluate positive selection using multiple nucleotide sequences alignment (phylip format) and maximum likelihood tree (newick format tree from RAxML).

I used branch site model by specifying model = 2 and NSsites = 2 and test by using null model (fix omega) and alternative model (estimate omega).

To make certain branch as foreground branch, I need to add #1 on that branch in tree files. I know which taxa I am interested in. If I want to label the branch representing smallest monophyletic group which contains the taxa I am interested in (see example below), how to do it automatically? Since I have hundreds of tree to run codeml, an automatic way to label trees is necessary. Also checking tree file that contains hundreds of taxa to find the branch is painful.

(    (A37:0.0392824443,A36:0.2301499674):0.0070550356,    (A35:0.0345817897,        (A34:0.0028844901,A33:0.0086649064):0.0413749361    ):0.0479157566)

For example, I am in interested in A35. The smallest monophyletic group contains A35: is

(A35:0.0345817897,        (A34:0.0028844901,A33:0.0086649064):0.0413749361    )

So I will add #1 behind that right parentheses. so the finally labeling should be

(    (A37:0.0392824443,A36:0.2301499674):0.0070550356,    (A35:0.0345817897,        (A34:0.0028844901,A33:0.0086649064)#1:0.0413749361    ):0.0479157566)
                                                          ^                                                           ^

But how can do it automatically?

codeml tree • 3.8k views
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the following Codeml wrapper could interest you: http://etetoolkit.org/docs/2.3/tutorial/tutorial_adaptation.html (Easy branch selection and inline visualization of results)

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also available as an interactive command line tool: http://etetoolkit.org/documentation/ete-evol/

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