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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.

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I would align your sequences with the software available here: https://github.com/veg/hyphy-analyses/tree/master/codon-msa

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  • $\begingroup$ That is a good approach and very up to date answer. $\endgroup$
    – M__
    Jun 19 '20 at 15:54
  • $\begingroup$ thank you i will try this out as well $\endgroup$
    – kcm
    Jun 19 '20 at 21:03
  • $\begingroup$ post-msa.bf is it like shell script? im seeing this extension for the first time $\endgroup$
    – kcm
    Jun 19 '20 at 21:05

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