Resolved; I hadn't taken into account the fact that I needed to scale my
trees by the clock rate.
On Thu, Feb 16, 2017 at 4:32 PM, William Gearty <wgea...@stanford.edu>
> Hi all,
> I've recently finished a tip-dating analysis (see
> https://firstname.lastname@example.org/msg04659.html) and
> I'm now trying to import the trees from the posterior (input.nex.run1.t,
> etc.) into R for some comparative analyses.
> Using read.nexus, I was able to successfully import the trees, but for
> some reason the branch lengths seem to be off.
> The branch lengths for the consensus tree (from sumt) appear to import
> into R fine (with the root at about 210 Ma), but the posterior trees seem
> to have root ages ranging from 43 to 147.
> Am I missing something in my MrBayes nexus file/analysis, which is causing
> the branch lengths to be off in the output file (I was under the impression
> branch lengths are by default printed with the trees)?
> Or is there a different (better) way to import them into R?
> Thanks in advance,
> William Gearty
> PhD Candidate, Paleobiology
> Department of Geological Sciences
> Stanford School of Earth, Energy & Environmental Sciences
PhD Candidate, Paleobiology
Department of Geological Sciences
Stanford School of Earth, Energy & Environmental Sciences
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