<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>

CC BY-SA 4.0
2020-06-19T15:54:13.380Z
That is a good approach and very up to date answer.
M__
CC BY-SA 4.0
2020-06-19T21:03:14.643Z
thank you i will try this out as well
kcm
CC BY-SA 4.0
2020-06-19T21:05:13.597Z
post-msa.bf  is it like shell script? im seeing this extension for the first time
kcm
CC BY-SA 4.0
2020-06-19T15:01:24.637Z
2020-06-19T15:01:24.637Z
Alex
<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>

<phylogenetics><perl>
Removing stop codons from alignment file for dn/ds calculation
# Removing stop codons from alignment file for dn/ds calculation

(Asked by: username_0 on 2020-06-12)

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.

**Tags:** phylogenetics, perl

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## 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  

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