This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Recombination And Positive Selection

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

codeml recombination
• 2,234 views • link
updated by Joseph Hughes Joseph Hughes • written by GR GR

Did you obtain your sequences via PCR + cloning?

• 0 views • link
written by Adrian Pelin Adrian Pelin

1 answer

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.

• 0 views • link
written by Joseph Hughes Joseph Hughes

Log in to answer this question.

More posts like this