Question: Constructing the ancestral state of amino acid
gravatar for RT
5.9 years ago by
European Union
RT350 wrote:

Hello Everyone,

I have the results from codeml analysis where I have identified few sites that are under positive selection in my target species. I am now looking for the change in amino acid in the nearest species and the ancestral amino acid. I have around 20 such genes where I have identified positive selection in orthologs of these genes. I can easily identify the amino acid in nearest species from the MSA of these genes. I am wondering if it is fair enough to identify the ancestral amino acid same way- looking at MSA for amino acid in the distant species retained in the orthology cluster. or there is any other way to construct the ancestral state of these sites?

I hope I am clear in asking the question.


selection codeml paml • 1.5k views
ADD COMMENTlink modified 5.8 years ago by Michael Dondrup48k • written 5.9 years ago by RT350
gravatar for Juke34
5.8 years ago by
Juke345.2k wrote:

You could try from the DNA sequence using the Ortheus tool. ( It allows to reconstruct the ancestral state of DNA sequences aligned. 

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Juke345.2k
gravatar for Michael Dondrup
5.8 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

FastML is a web server for ancestral sequence reconstruction, using the sequence MSA plus phylogenetic tree as input. I don't know if that answers your question, but I have seen papers that use both PAML and FastML and compare the results.

ADD COMMENTlink written 5.8 years ago by Michael Dondrup48k
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