This might be of interest for various R phylogenetics programmers: there's
currently no package to access this info.
Title
Tree-for-All: A hackathon to access OpenTreeâs global phylogeny resources
Content
A global âtree of lifeâ will transform biological research in a broad range
of discipli
Hello,
There is a program called "Path-O-Gen" (http://tree.bio.ed.ac.uk/software/pathogen/)
which can (among other things) reroot a phylogeny with dated tips in the location most compatible
with the assumption of a strict molecular clock, by using root-to-tip regression (Rambaut, Andrew.
"Esti
Hi,
if anyone else (especially Linux users) would have similar problem with GIT
and/or zipped package, this is the issue
https://github.com/hadley/devtools/issues/406 It also contains useful link how
to solve it. Basically, set unzip command in appropriate R option or download
zip, unzip it at
Thankyou very much to all for your effort in improving the function!
all the best
paoo
Da: Liam J. Revell
Inviato: martedì 10 giugno 2014 15.13
A: Jonas Eberle; Paolo Piras; r-sig-phylo@r-project.org
Oggetto: Re: edge color in phylomorphospace3d
Thanks Jon
Thanks Jonas.
I had just added this to phytools. Not yet on CRAN but more details
(including how to use it) can be seen here:
http://blog.phytools.org/2014/06/coloring-edges-in-phylomorphospace3d.html.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachuse
Hi,
if anyone else would have problem with non-diploids and poppr, install
developmental version from the GIThub repository. Many thanks to authors for
pointing me right direction and writing this nice package. :-)
All the best,
Vojtěch
Dne Po 9. června 2014 14:36:23 jste napsal(a):
> Hi,
> I li
Hi,
So I tried to play with the code you gave me… then trying to adapt it, I notice
that I don't know if it is possible to make several group with several color…
and actually I'm not identification sample and groups one by one, but I already
have an object telling every groups.
Is that poss
Hi Dan,
Thanks for your reply. Indeed, I did some simulations under BM and
depending on the variance we have an inflated Type I error ranging from 5
to 25%. Subsampling the dataset may work, although our trees are not that
large (300 to 500 tips), so the power will be reduced substantially. I am
v
Dear Paolo,
I modified the phylomorphospace3d code some time ago to be able to plot
colored branches (see below). You can use pointcol and edgecol to color the
plot. These can be simple color specifications (such as "black") or vectors
of colors that have the length of your number of tips or edges
