Geiger has an interface to pathd8; it has the beginnings of interfaces to
other programs, too, but I don't think they're finished yet.
Best,
Brian
___
Brian O'Meara
Associate Professor
Dept. of Ecology & Evolutionary Biology
U. of Tennessee, Knoxville
http://ww
Hi Fabian,
If the goal is to get an ultrametric tree from your sequences, and not
really date the divergences among them, you may consider using a UPGMA
tree. Another solution is to use chronoMPL in ape which implements the
mean path length method; the advantage of this one is that it takes th
Hi Roger,
Fast Solution: use pathd8 or r8s or treePL. Not in R... pathd8 should be the
easiest one since you just need a ultrametric tree... 1 sec in parthd8
Cheers, Franz
> On 21.09.2015, at 16:21, Fabian Roger wrote:
>
> hej everyone
>
> I have a large phylogeny based on 16S RNA OTU data
hej everyone
I have a large phylogeny based on 16S RNA OTU data (> 7000 OTUs). In order to
calculate some metrics of phylogenetic diversity I need to make the tree
ultrametric. I thought about using the chronos function from the ape package in
R.
However I run into two problems: the main pro
