Multigene family analysis with codeml

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Rafael Della Coletta

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Nov 25, 2017, 3:59:32 PM11/25/17

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Hello,

I am a beginner in the field of phylogenetics, and I want to estimate dS:dN ratio and selective pressure in a multigene family.

I already built a maximum likelihood phylogenetic tree showing the relationship of 8 genes in 15 species (some species don't have some of the genes, while others have many duplications). However, from what I have been reading, I understand that it may not be possible to estimate that ratio with so many genes involved. Thus, the idea was to run codeml for each gene separately. However, some genes are very close to each other and belong to the same monophyletic clade, so I don't think I can separate them in the analysis.

Any thoughts on how should I proceed?

If you know any useful literature for estimating selective pressure in multigene families, it would be very much appreciated as well.

Thank you very much!

Rafael.

Ziheng

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Mar 27, 2018, 4:00:56 PM3/27/18

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if they are different genes, with different functions, they should be analyzed as separate datasets.

here are a few review -like reading materials:

Yang Z. 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586-1591.

Anisimova M, Kosiol C. 2009. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol Biol Evol 26:255-271.
chapter 11 in Yang Z. 2014. Molecular Evolution: A Statistical Approach. Oxford University Press, Oxford, England.