Dear Emmanuel and Alejandro
Many thanks for your replies.
Emmanuel, I understand what you said if I use vcv(nonultrametric_tree,
cor=FALSE) in a phylogenetic comparative method (PCM). But if I use
vcv(nonultrametric_tree, cor=TRUE), isn't this the same as assuming a
ultrametric tree? I may be mis
Hi,
I would venture in adding that with an additive tree the differences in evol
rates among species are determined by the genes used to estimate the tree,
given differences in substitution rates among genes. I do think its important
to bear in mind.
Cheers
Alejandro
Alejandro Gonzalez Voye
Sure they are different. I forgot to mention that.
In comparative analyses, the expected quantity of trait change (= the
variance in the VCV matrix) is given by the product of the rate of
evolution of the trait with branch length. So using a non-ultrametric
tree is a way to assume different ra
Dear Emmanuel
Many thanks for your swift reply.
If we get a correlation matrix, via chronoMPL [i.e.
vcv(chronoMPL(nonultrametric_tree,cor=T))], this correlation matrix is
different from a correlation matrix obtained directly from vcv [i.e.
vcv(nonultrametric_tree, cor=T)].
Could you enlighten m
Dear List
I would like to thank everyone in the list.
Could any one show me in detail How I can download the molecular dat from
TreeBase and analyse it using APE.
Many thanks in advance.
Sami Rabei
--
With my Best Wishes
Sami Hussein Rabei (PhD)
Botany Department,
Dear Shinichi,
A fast solution is provided by the function chronoMPL in ape; it does
not require calibration points (see the references in the help page of
this function for the assumptions). The function chronos (also in ape)
is another possibility but it needs at least one calibration point
Hi,
This kind of issue was reported some time ago and there is an item in
ape's FAQ:
http://ape-package.ird.fr/ape_faq.html#Bayestrees
But your situation seems a bit different. You may also check the tree
with checkValidPhylo() to have a diagnostic of what's wrong.
Best,
Emmanuel
Le 28/1
