Hi Kellen.

I'm not sure if this is still relevant, but I just posted source code (http://www.phytools.org/read.newick/v0.4/read.newick.R) for a function that will read this type of Newick string (i.e., with node labels & singletons) into R. To create the attached plot I had to first collapse singles, i.e.,

require(phytools)
source("read.newick.R")
tree<-read.newick(file="output.txt")
tree<-collapse.singles(tree)
plotTree(tree,type="fan")

All the best, Liam

Liam J. Revell, Assistant 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 6/6/2013 4:25 PM, Megan Bartlett wrote:
Dear Kellen,

It looks to me like the problem is that you have genera labels containing
only one species, like (Sabatia_angularis:46.296295)sabatia. The
frustrating thing about this notation is that Phylocom is fine with this,
but R can't read it, even though it's technically legal in the Newick
format. I don't think collapse.single would solve your problem, since R
isn't even able to input the file to perform a function on it. For
troubleshooting, I would try running clean.phylo on this tree in Phylocom,
and seeing if that solves your problem. If so, I would run clean.phylo on
your undated tree before you run BLADJ. (This would be your Phylomatic
output if you assembled your undated tree with Phylomatic). Because having
node ages for singleton taxa will not affect your branch lengths for that
taxa (for example, Sabatia angularis will have the same branch length
whether or not you have an age for the genus Sabatia), you should get the
same results. I believe the Phylocom manual discusses this in the
Phylomatic section.

Best,

Megan

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