Question: Recombination And Positive Selection
0
gravatar for RT
6.8 years ago by
RT350
European Union
RT350 wrote:

Hi All,

As recombination events can be misinterpreted as selective pressure events. Is it right to remove the seq identified with recombination events from MSA of your gene family before running codeml?

Thanks, R

recombination codeml • 1.3k views
ADD COMMENTlink modified 6.8 years ago by Joseph Hughes2.8k • written 6.8 years ago by RT350

Did you obtain your sequences via PCR + cloning?

ADD REPLYlink written 6.8 years ago by Adrian Pelin2.4k
0
gravatar for Joseph Hughes
6.8 years ago by
Joseph Hughes2.8k
Scotland, UK
Joseph Hughes2.8k wrote:

Recombination can indeed result in misinterpretations in selection analyses. One approach is to first identify the recombination breakpoints in your multiple sequence alignment (MSA). You can then create partitions of your MSA that are recombination free and analyses these separately in codeml.

ADD COMMENTlink written 6.8 years ago by Joseph Hughes2.8k
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