Re: [R-sig-phylo] AGY coding
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 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
>
> 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
> 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
>>
>> [[alternative HTML version deleted]]
>>
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>>
>
>
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Re: [R-sig-phylo] AGY coding
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
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 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
>
> [[alternative HTML version deleted]]
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-ph...@r-project.org/
>
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[R-sig-phylo] AGY coding
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 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
