Hi all,
I just uploaded a new version of phangorn (1.99-7), which does not depend
on the rgl package. This should allow phangorn to work on all platforms
again. It seems midpoint (phangorn) and midpoint.root (phytools) give the
same result, which is reassuring. midpoint seems to be faster for
Hi Todd.
Challenge accepted ;)
Try the attached code. In my tests it returns the exact same result as
midpoint in phangorn, but it does not use any phangorn code internally.
(It does depend on phytools dependencies, particularly ape.) It is
probably much less elegant slower than phangorn
Liam said:
Joe's correct that this is not yet in our project to create an R interface
for PHYLIP (Rphylip, https://github.com/liamrevell/Rphylip). As soon as I
get a chance to work on this project today, I will add it.
That may be hard to do, as Retree is interactive and
has two levels of
All,
As an update: the script that Liam wrote for midpoint rooting seems to
have worked well for us. I did not numerically test the rooting results,
but they pass the eye test (ie they look right to me). I serially
rooted about 100 trees with 50-250 OTU's each, and it was fast, so it
was
