Hello John,
it seems the chronogram contains the heights instead of the
edge.lengths for each edge.
Here is a small function to convert the tree. You should check if it
is the same as in treefinder.
convert.tree <- function(tree){
el = numeric(max(tree$edge))
el[tree$edge[,2]] = tree$edge.length
el[min(tree$edge[,1])] = tree$root.edge
tree$edge.length = el[tree$edge[,1]] - el[tree$edge[,2]]
tree
}
tree = read.tree("chrono3.tree")
tree2 = convert.tree(tree)
plot(tree2)
Regards,
Klaus
On 4/26/12, John Denton <[email protected]> wrote:
> Hi folks,
>
> I generated a quick chronogram in TreeFinder (attached) for an exploratory
> analysis in R. The tree appeared fine in the Treefinder plot window, but the
> branch length notation does not appear to be compatible with R plotting for
> a chronogram.
>
> The basal divergence time is 33.9 MYA (which appears in the Newick file),
> but FigTree is telling me the base is something around 22. Has anyone else
> encountered the problem with TreeFinder chronograms? Does anybody have a
> suggestion for how to rescale? I'd prefer to use this tree rather than
> simply make the original unrooted tree ultrametric.
>
> Thanks!
>
> ~John
>
>
> John S. S. Denton
> Ph.D. Candidate
> Department of Ichthyology and Richard Gilder Graduate School
> American Museum of Natural History
> www.johnssdenton.com
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