text: user285: This is one of the question which is very similar to my problem or almost same to my problem 
  I ran with dummy data nucleotide alignment and the amino file it works perfectly fine,i can run the dn/ds from phangorn without any issue.
  But when i ran with my data nucleotide alignment and the amino file I do get this warning 
  In kaks(carps) : sequence lengths are not a multiple of 3
  
  and error.
  The code 
  Any help or suggestion would be highly appreciated.
  
  user9051: I would align your sequences with the software available here: https://github.com/veg/hyphy-analyses/tree/master/codon-msa
  
original_text: 285: <p>This is one of the <a href="https://www.biostars.org/p/65618/#443249" rel="nofollow noreferrer">question</a> which is very similar to my problem or almost same to my problem </p>
  
  <p>I ran with dummy data nucleotide <a href="https://drive.google.com/file/d/1XfmKO4GZPsSNonhcpwVK5iN5LDd-LS4L/view?usp=sharing" rel="nofollow noreferrer">alignment</a> and the amino <a href="https://drive.google.com/file/d/1gbBgaGNOrXgVjZzNxvNCizLq0n3LL5Lj/view?usp=sharing" rel="nofollow noreferrer">file</a> it works perfectly fine,i can run the dn/ds from phangorn without any issue.</p>
  
  <p>But when i ran with my data nucleotide <a href="https://drive.google.com/file/d/1I_8eCQlNG0r3vdVpkoGmKJEatmovgF9z/view?usp=sharing" rel="nofollow noreferrer">alignment</a> and the amino <a href="https://drive.google.com/file/d/1kJapQ9UyCPnIr8uIkLi8zrvlT5NGCj-d/view?usp=sharing" rel="nofollow noreferrer">file</a> I do get this warning </p>
  
  <pre><code>In kaks(carps) : sequence lengths are not a multiple of 3
  </code></pre>
  
  <p>and error.</p>
  
  <p>The <a href="https://drive.google.com/file/d/14s4YnTPoQPL0fkGxNEklUYrhPoyhxh4C/view?usp=sharing" rel="nofollow noreferrer">code</a> </p>
  
  <p>Any help or suggestion would be highly appreciated.</p>
   9051: <p>I would align your sequences with the software available here: <a href="https://github.com/veg/hyphy-analyses/tree/master/codon-msa" rel="nofollow noreferrer">https://github.com/veg/hyphy-analyses/tree/master/codon-msa</a></p>
  