Removing stop codons from alignment file for dn/ds calculation 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.
I would align your sequences with the software available here: https://github.com/veg/hyphy-analyses/tree/master/codon-msa