text: user285: 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.
  
  user3848: 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.
  
original_text: 285: <p>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. </p>
  
  <p>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.</p>
  
  <p>So now i have to associate nucleotide mutation with amino acid sequence data.</p>
  
  <p>Any suggestion or help would be really appreciated. As always if there is a <code>R</code> way to performing the analysis then it would be really good.</p>
   3848: <p>I  would output the aligned nucleotide sequences and input them into an alignment editor such as <code>Sequtron</code> (Mac), <code>MEGAX</code>(particularly PC) or <code>Jalview</code> (Linux). </p>
  
  <p>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 <code>R</code> equivalent that I am aware of.</p>
  
  <p>More generally I would do a non-synonymous / synonymous analysis which <code>fangorn</code> 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.</p>
  
  <p>There are character mapping approaches which will map an amino acid mutation onto a phylogeny as an alternative.</p>
  