(cough) Well, I for one never saw your original email, Will. At least
from my perspective, it looks like it never made it to the list.

Um, well, what are you trying to obtain? A supertree analysis that
thinks about the stratigraphic order of taxa? This sounds like your
trying to create some stratocladistic parallel to supertree analyses.
And no offense to either the stratocladistics and supertree
communities, but that doesn't seem like a winning combination.

My recommendation (currently) is maybe try tip-dating without a
morphological matrix, with the topology constrained relative to their
input topology. I haven't tried this myself, but I know some others
have. My package paleotree has a function for converting a tree in R
into a set of constraints for MrBayes. At least on paper,
character-less tip-dating should be like doing cal3... in practice,
though, I have no idea what will happen. Maybe it will have the same
problems as your cal3 trees, maybe it won't.

I hope this helps,
-Dave

On Wed, Oct 5, 2016 at 2:41 PM, William Gearty <wgea...@stanford.edu> wrote:
> Hmm, so I'll take it that this doesn't exist yet?
>
> On Thu, Sep 8, 2016 at 10:28 AM, William Gearty <wgea...@stanford.edu>
> wrote:
>
>> Hi all,
>>
>> I'm currently working with a supertree to perform some comparative
>> analyses.
>> Of course, I have to time-scale the tree to perform the analyses I have in
>> mind, and to do that I'm using the cal3 method from paleotree.
>>
>> However, after trying different parameter values and some conversations
>> with Dave Bapst, it looks like my supertree is fairly incongruent with the
>> stratigraphic constraints I've supplied.
>> Of course, I could just take the paleotree output as it is now and run the
>> analyses (zero-length branches and all), but that seems like a bad thing to
>> do.
>>
>> So, I figured I would build a new supertree that better fits the
>> stratigraphic constraints of the various taxa.
>> However, I'm at a loss of how to do that.
>> I figured there would be a package or software that would be able to
>> accomplish this, but so far I've come up with nothing (perhaps I'm
>> searching for the wrong thing?).
>>
>> Which is where this list comes in: are any of you aware of an R package
>> (or other software) that can build a supertree using multiple source trees
>> and stratigraphic constraints?
>> If not, any thoughts on how I should get started?
>>
>> Thanks in advance,
>> Will
>>
>> --
>> William Gearty
>> PhD Candidate, Paleobiology
>> Department of Geological Sciences
>> Stanford School of Earth, Energy & Environmental Sciences
>> people.stanford.edu/wgearty
>>
>
>
>
> --
> William Gearty
> PhD Candidate, Paleobiology
> Department of Geological Sciences
> Stanford School of Earth, Energy & Environmental Sciences
> people.stanford.edu/wgearty
>
>         [[alternative HTML version deleted]]
>
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-- 
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701

http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html

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