visualize amino acid changes in genes that are positively selected after codeml run

Question

[Mehmet]

Dear All,

can anyone suggest a tool/software to visualize amino acid changes of positively selected genes? I have run codeml and detected positively selected genes, and now I want to produce 3D graphs of genes by emphasizing amino acid changes.

Do you know any tool or software for this?

[Joe]

This is not specifically what you asked for, but you can create an attributes file, and render the 3D structure of the protein by selection in UCSF Chimera, if you have a 3D structure for that protein.

(see https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html )

Answer 1

[h.mon]

The ETE3 toolkit wraps codeml and, in addition to performing selection tests, it produces some nice figures. It also has an interactive GUI mode where one can customize / explore the analyses and graphics. For examples, see:

http://etetoolkit.org/documentation/ete-evol/

http://etetoolkit.org/docs/latest/tutorial/tutorial_adaptation.html

http://etetoolkit.org/cookbook/ete_evol_codeml_configuration_files.ipynb

I am not sure what you mean by "3D graphs of genes by emphasizing amino acid changes", though. Are you talking about protein structure?

[Mehmet]

Thank you for your suggestions. I mean I want to show where amino acid changes of a protein occurred due to positive selection.