I am constructing a phylogeny of frogs from Western ghats India and I am using two genes- 16SrRNA and NADH. Since NADH is a protein coding gene,I believe there will be stop codons. Is it necessary to remove the codons before the analysis? will it affect the the final topology of the phylogenetic tree?
The short answer is no, don't worry about the stop codons. They will not alter the final topology of your best tree.
It might be possible to argue that the stop codons would be under stabilizing selection and therefore may provide little phylogenetic information because point mutations are extremely deleterious. However, in the end that should matter very very little due to the amount of data you should get from the rest of the sequence. Also, depending on how the sequences were generated (targeted gene cloning or phylogenetics) there is no guarantee that the stop codons are included in those reads.
If anything having stop codons might make it easier to align the sequences.
Hi Priti,
it depends where you encounter the stop codons. If you have the full sequence and heve the stop codon at the end (where it is expected) you are fine. But if you have internal stop codons, ones that would lead to shorter proteins, you have a problem. The stop codon itself does not affect the topology of the phylogenetic tree, however, such internal stop codons may indicate that you sequence a peudogene and not your targeted gene copy. This would greatly compromise the outcome and reliability of your topology. So you should make sure that none of your sequences have internal stop codons, or remove such sequences.
Best, Martin