[R-sig-phylo] AGY coding

Discussion:

Karla Shikev

2018-08-24 14:36:26 UTC

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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Joseph Brown

2018-08-24 19:52:56 UTC

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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

Post by Karla Shikev
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]]
_______________________________________________
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-

[[alternative HTML version deleted]]

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Karla Shikev

2018-08-26 21:40:51 UTC

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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

Post by Joseph Brown
Hi Karla.
Not sure how you have your sequences stored, but if as a string you can do
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