Hi Karla.

Not sure how you have your sequences stored, but if as a string you can do
it yourself:

str <- gsub("C|T", "Y", str);

As for RY vs. AGY, this paper
<https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-S2-S8>
is very nice. Basically, if you are using them for phylogenetic inference
it may be that recoding destroys the Markovian property of the alignment,
and that may mislead you downstream. A very interesting consideration that
I feel is not widely known.

HTH.
JWB


On Fri, Aug 24, 2018 at 3:36 PM, Karla Shikev <karlashi...@gmail.com> wrote:

> Dear all,
>
> Does anyone have a function for AGY coding of nucleotides?
>
> By the way, any thoughts on using RY- vs AGY-coding?
>
> Thanks!
>
> Karla
>
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