To begin with I have two nucleotide sequence to compare I want to see how they might have evolved in terms of sequence similarity and differences. One of the way i can think of is align the sequences. But i m not getting how do i associate it with mutation.

Now question is how do i know about mutation. I have the respective amino acid data from which i know there been mutation which is making changes how the binding happens between two sequences.

So now i have to associate nucleotide mutation with amino acid sequence data.

Any suggestion or help would be really appreciated. As always if there is a R way to performing the analysis then it would be really good.

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    $\begingroup$ Are you familiar with non-synonymous vs synonymous analysis and is this part of the phangorn package? $\endgroup$ – Michael Jun 2 at 11:58
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    $\begingroup$ You must have done an alignment to generate the phangorn tree and if you have branches and stuff you must have mutations. An alignment viewer that converts in and out of amino acid translation is a place to start $\endgroup$ – Michael Jun 2 at 22:08
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    $\begingroup$ yes i have done mutation and i have the tree as well ."An alignment viewer that converts in and out of amino acid translation" jalview would be a good start i guess.. $\endgroup$ – krushnach Chandra Jun 2 at 22:34
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    $\begingroup$ Cool, I will sketch a few ideas below when I have a minute $\endgroup$ – Michael Jun 3 at 6:23
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    $\begingroup$ that would be really kind of you $\endgroup$ – krushnach Chandra Jun 3 at 8:31

I would output the aligned nucleotide sequences and input them into an alignment editor such as Sequtron (Mac), MEGAX(particularly PC) or Jalview (Linux).

The alignment editors will allow you to flick between the triplet codon and the amino acid sequence. Therefore spotting which triplet codon mutations associate with each given amino acid mutation is easy.There is no R equivalent that I am aware of.

More generally I would do a non-synonymous / synonymous analysis which fangorn will perform. This assesses the number of mutations in which cause an amino acid change against the number of mutations that cause a 'silent' mutation (no amino acid change). A synonymous phylogeny will represent all mutations which don't change the tree. A non-synonymous phylogeny is the same as an amino tree.

There are character mapping approaches which will map an amino acid mutation onto a phylogeny as an alternative.

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  • $\begingroup$ I did run the kaks but ran into this bioinformatics.stackexchange.com/questions/13499/… $\endgroup$ – krushnach Chandra Jun 9 at 14:47
  • $\begingroup$ Hi @krushnachChandra I've answered your question. Why it fails is easy, but correcting it is more complication, however this is needed before any form of amino acid to nucleotide mutation analysis can take place. $\endgroup$ – Michael Jun 9 at 15:05

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