Hi Martin.
Since you are writing & reading trees to file, my guess is that it has
to do with numerical precision - that is, the rounding of your edge
lengths when they are written to file.
Does your tree look ultrametric when plotted in R? If so, this is
probably the case.
My recommendation is that you use phangorn to compute the non-negative
least-squares edge lengths with the condition that the tree is
ultrametric. This will give you the edge lengths that result in the
distances between taxa with minimum sum of squared differences from the
distances implied by your input tree, under the criterion that the
resulting tree is ultrametric.
To do this you need to merely run:
library(phytools)
library(phangorn)
is.ultrametric(tree) ## fails
plotTree(tree,ftype="off") ## does my tree look ultrametric?
nnls<-nnls.tree(cophenetic(tree),tree,rooted=TRUE)
is.ultrametric(tree) ## should pass
Let us know if this works. All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 8/16/2016 6:41 AM, Martin Dohrmann wrote:
Hi,
I want to do some diversification pattern analyses with various R packages. I'm using a
time-calibrated tree produced by PhyloBayes. Branch lengths are in millions of years and all taxa
are extant, so the tree should be ultrametric. However, when I call "is.ultrametric", it
returns "FALSE".
Has anybody encountered something like this? Any ideas about what's going
on/how to solve this?
Some further information:
I also tried other PhyloBayes time trees, with the same result. In contrast, MrBayes time
trees I tried for comparison are recognized as ultrametric. Regarding my diversification
analyses, TESS would not run, telling me "The likelihood function is only defined
for ultrametric trees!". On the other hand, BAMMtools doesn't seem to have a problem
with my tree. I haven't tried other packages yet, but I suspect RPANDA, TreePar etc.
might also have issues if they don't recognize my tree as ultrametric.
I'd appreciate any help!
Best wishes,
Martin
Dr. Martin Dohrmann
Ludwig-Maximilians-University Munich
Dept. of Earth & Environmental Sciences
Palaeontology & Geobiology
Molecular Geo- & Palaeobiology Lab
Richard-Wagner-Str. 10
80333 Munich, Germany
Phone: +49-(0)89-2180-6593
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