Recombination And Positive Selection

Question

[GR]

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

[Adrian Pelin]

Did you obtain your sequences via PCR + cloning?

Answer 1

[Joseph Hughes]

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.