Codeml To Study Selection Pressure

Question: Codeml To Study Selection Pressure

8.4 years ago by

RT • 350

European Union

RT • 350 wrote:

Hi All,

Just few quick questions about Codeml.

Can we study lineage-specific selection only on sequences that are single copy orthologs (or in simple words just have 1-1 relations). What should I do in case of multigene families? Does codeml works well in case of multi gene families? Do I have to extract 1-1 relations from these families and then input to codeml or the whole family can go as input?

Thanks, RT

evolution selection • 1.9k views

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modified 8.4 years ago by DG ♦ 7.2k • written 8.4 years ago by RT • 350

8.4 years ago by

DG ♦ 7.2k

DG ♦ 7.2k wrote:

The short answer is that, it really all depends on what you want to look at. There have been a series of papers out recently by Marc Robinson-Rechavi, Matthew Hahn, and a few others recently about selection and orthology/paralogy and the notion that orthologs should be more similar to one another functionally than paralogs. Ideally yes, I think you should extract the 1-to-1 ortholog relationships and look at selection pressures between those, but it really all depends a bit on what question you are trying to address.

ADD COMMENT • link written 8.4 years ago by DG ♦ 7.2k

Thanks Dan. I know the best approach would be to identify 1-1 ortholog and then study the selection pressure.

In my case, I have 200 genes so it is difficult to identify 1-1 relation for all the genes. We just want to give a general statement whether our gene set is under selection or not. Do you have any useful reference for studying selection on entire gene families using codeml? and reference for codeml used for such a large dataset will also be a great help.

Thanks once again. Reetu

ADD REPLY • link modified 8.4 years ago • written 8.4 years ago by RT • 350

Hi Dan, could you edit your post and include some links to those papers? I would find those papers very helpful. Thanks.

ADD REPLY • link written 8.4 years ago by SES ♦ 8.4k

This was the most recent paper "resolving" the ortholog conjecture: http://www.ncbi.nlm.nih.gov/pubmed/22615551

It references the Hahn and earlier papers so is probably the best starting place.

ADD REPLY • link written 8.4 years ago by DG ♦ 7.2k

Excellent! Thanks for the response.

ADD REPLY • link written 8.4 years ago by SES ♦ 8.4k

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