Answers.Body: <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>
  
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Answers.Text: That is a good approach and very up to date answer.
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Answers.Text: thank you i will try this out as well
Answers.UserDisplayName: kcm
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Answers.Text: post-msa.bf  is it like shell script? im seeing this extension for the first time
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Body: <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>
  
Tags: <phylogenetics><perl>
Title: Removing stop codons from alignment file for dn/ds calculation
ThreadText: # Removing stop codons from alignment file for dn/ds calculation
  
  (Asked by: username_0 on 2020-06-12)
  
  This is one of the [question](https://www.biostars.org/p/65618/#443249) which is very similar to my problem or almost same to my problem
  
  I ran with dummy data nucleotide [alignment](https://drive.google.com/file/d/1XfmKO4GZPsSNonhcpwVK5iN5LDd-LS4L/view?usp=sharing) and the amino [file](https://drive.google.com/file/d/1gbBgaGNOrXgVjZzNxvNCizLq0n3LL5Lj/view?usp=sharing) it works perfectly fine,i can run the dn/ds from phangorn without any issue.
  
  But when i ran with my data nucleotide [alignment](https://drive.google.com/file/d/1I_8eCQlNG0r3vdVpkoGmKJEatmovgF9z/view?usp=sharing) and the amino [file](https://drive.google.com/file/d/1kJapQ9UyCPnIr8uIkLi8zrvlT5NGCj-d/view?usp=sharing) I do get this warning
  
  ```
  In kaks(carps) : sequence lengths are not a multiple of 3
  
  ```
  
  and error.
  
  The [code](https://drive.google.com/file/d/14s4YnTPoQPL0fkGxNEklUYrhPoyhxh4C/view?usp=sharing)
  
  Any help or suggestion would be highly appreciated.
  
  **Tags:** phylogenetics, perl
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-06-19. Score: 2
  
  I would align your sequences with the software available here: <https://github.com/veg/hyphy-analyses/tree/master/codon-msa>
  
  > **Comments:**
  > **username_2**: That is a good approach and very up to date answer.  
  > **username_0**: thank you i will try this out as well  
  > **username_0**: post-msa.bf  is it like shell script? im seeing this extension for the first time  
  
  ---
  
  