Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-09T14:47:56.293Z
Answers.Text: I did run the kaks but ran into this https://bioinformatics.stackexchange.com/questions/13499/calculating-synonymous-and-non-synonymous
Answers.UserDisplayName: kcm
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Answers.Text: 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.
Answers.UserDisplayName: M__
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Answers.CreationDate: 2020-06-06T20:38:18.450Z
Answers.LastActivityDate: 2020-06-06T20:44:47.133Z
Answers.LastEditDate: 2020-06-06T20:44:47.133Z
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Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-02T11:58:20.333Z
Comments.Text: Are you familiar with non-synonymous vs synonymous analysis and is this part of the phangorn package?
Comments.UserDisplayName: M__
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Comments.CreationDate: 2020-06-02T17:37:50.267Z
Comments.Text: i did come to read that let me explore it..will get back
Comments.UserDisplayName: kcm
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-02T18:33:21.233Z
Comments.Text: Thats probably what you want ... depends on your investigation
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-02T21:29:38.000Z
Comments.Text: so my simple idea is compare the respective nucleotide sequence and see if there exist a mutation if yes then do the same in the protein sequence. So to see mutation I'm not sure how to start ..alignment perhaps not sure though..how to approach it..
Comments.UserDisplayName: kcm
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-02T22:08:40.890Z
Comments.Text: 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
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-02T22:34:49.070Z
Comments.Text: 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..
Comments.UserDisplayName: kcm
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-03T06:23:41.213Z
Comments.Text: Cool, I will sketch a few ideas below when I have a minute
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-06-03T08:31:34.687Z
Comments.Text: that would be really kind of you
Comments.UserDisplayName: kcm
Tags: <r><phylogenetics><sequence-analysis>
Title: Compare nucleotide mutation with amino acid
ThreadText: # Compare nucleotide mutation with amino acid
  
  (Asked by: username_0 on 2020-06-01)
  
  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.
  
  **Tags:** r, phylogenetics, sequence-analysis
  
  > **Comments:**
  > **username_1**: Are you familiar with non-synonymous vs synonymous analysis and is this part of the phangorn package?  
  > **username_0**: i did come to read that let me explore it..will get back  
  > **username_1**: Thats probably what you want ... depends on your investigation  
  > **username_0**: so my simple idea is compare the respective nucleotide sequence and see if there exist a mutation if yes then do the same in the protein sequence. So to see mutation I'm not sure how to start ..alignment perhaps not sure though..how to approach it..  
  > **username_1**: 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  
  > **username_0**: 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..  
  > **username_1**: Cool, I will sketch a few ideas below when I have a minute  
  > **username_0**: that would be really kind of you  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-06-06. Score: 1 | Accepted answer
  
  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.
  
  > **Comments:**
  > **username_0**: I did run the kaks but ran into this https://bioinformatics.stackexchange.com/questions/13499/calculating-synonymous-and-non-synonymous  
  > **username_1**: 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.  
  
  ---
  
  