Hi Mattia,
The saturation plot is a classic exercise with ape: see ?dist.dna. This
function allows you to count the numbers of Ts or Tv, or any kind of
distances. Then using standard plot commands in R, you can make your own
satutation plots easily.
See ?delta.plot in ape for another method.
Best,
Emmanuel
Le 10/05/2014 11:29, Mattia Prosperi a écrit :
Hi all,
I know there's plenty of methods (many already available in R) to evaluate
phylogenetic signal of a tree with respect to a character.
But I have found the term 'phylogenetic signal' also in the context of a
sole alignment/tree without the presence of associated characters. For
instance, a way to measure such signal is to compute Tv/Tr ratio vs.
divergence plots, to look at saturation, as the function for assessing
substitution saturation (Xia, Xie, Salemi, et al. 2003; Xia and Lemey
2009), or also to perform a likelihood mapping of quartet trees (using
TREEPUZZLE). These measures give ideas about the suitability of the
sequence alignment for inferring trees, and when looking at possible tree
topologies, how many conflicting topologies are present (which may give
hints on recombination, among other things).
I was wondering if there were similar/equivalent tests implemented in R.
Thanks.
M.P.
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