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DNA seq of non-equal length for the dna.dist() [ reply ]
By: Mathilde Dahl on 2016-03-03 13:52
Hi Help-forum for SPIDER (this is what this is, right?)

I get this error:

"DNA sequence in list not of same length"

when trying to run the dna.dist() function.

I don't understand why the DNA seq need to be of same length? - unless of cause they are not being aligned with this function?

I tried to combine the calculations with the pairwiseAlignment() function from the Biostrings package, but the alignment score, cannot be directly be replaced with the the distance score, as this is not a value between 1-0, then I will have to manipulate the alignment score.... So at this point, I thought I would ask if there is a better way to implement an alignment and/or an acceptance of unequal sequence length for the dna.dist() function?

I apologize, if this is nonsense, my brain has been chewing on this for some hours now, and I know this can be bad :)

Kind regards,

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