Hi Alina.
Since you mentioned some functions of phytools, I thought it might be
helpful to describe what each function is actually doing:
1) The function ls.consensus computes a least-squares (LS) consensus
tree. This is the LS tree on the average patristic distance matrix of
the input trees,
Le 25/01/2019 à 00:14, Alina van dijk a écrit :
Hi everyone,
Thanks Emmanuel and Joseph for sharing your thoughts!
Emmanuel, today I tried multi2di and it works. But, if I understand
correctly, this function transforms the dichotomies with branches of
length zero. So for me, in fact, doesn't
Hi Alina,
I'm not entirely sure I understand the problem, but perhaps
phangorn::maxCladeCred() could help?
I have used at some point to summarize 100 posterior mammal trees, and got
a binary ultrametric tree. Note that my input trees were also fully binary
and ultrametric, so if your results may
Hi everyone,
Thanks Emmanuel and Joseph for sharing your thoughts!
Emmanuel, today I tried multi2di and it works. But, if I understand
correctly, this function transforms the dichotomies with branches of length
zero. So for me, in fact, doesn't solve the politomy. Right?
Joseph, I'm only a
Hi Alina,
Did you try multi2di() to remove polytomies?
Best,
Emmanuel
Le 23/01/2019 à 17:41, Alina van dijk a écrit :
Hi everyone,
My name is Alina, I'm attending master degree in ecology and I have a
little problem with my consensus phylogeny. I used 1000 phylogeny of
birdtree to construct
I typically use a non-R tool like treeannotator (from the BEAST package)
to do this type of thing, especially when involving large numbers of big
trees.
HTH.
Joseph.
On Wed, Jan 23, 2019 at 4:42 PM Alina van dijk wrote:
> Hi everyone,
>
> My name is Alina, I'm attending master degree in
