Hi Joseph,
The object is stored as DNAbin.
Thanks for the paper. Some of the tips on my phylogeny have very biased GC
content and I was planning on using some sort of recoding (RY or AGY), but
the paper you mentioned makes some important points.
Karla
On Fri, Aug 24, 2018 at 4:52 PM Joseph Brown <josep...@umich.edu> wrote:
> 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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>>
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