Hi all,
ape's web site has been moved to this URI:
http://ape-package.ird.fr/
(Currently, the redirection from the old URI does not work correctly.
I hope it will be fixed soon.)
Regarding the issue of "singleton nodes and phylomatic", this is
mentioned in ape's FAQ (FAQ #15) but in a different way than
originally asked by Kellen. I have added a link to Megan's excellent
post.
Supporting singleton nodes is one feature that might be included in
ape in the future (among many others).
Best,
Emmanuel
Fri, 7 Jun 2013 00:32:58 -0400 "Liam J. Revell" <[email protected]>:
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: [email protected]
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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