# Re: [R-sig-phylo] Randomly Resolved Polytomies

```Liam,

Thanks so much for your reply and for the blog post, I was able to get it
working.```
```
-Laura

On Wed, Jun 21, 2017 at 10:35 AM, Liam J. Revell <liam.rev...@umb.edu>
wrote:

> Dear Laura.
>
> I also just posted a possible solution to my blog here:
> http://blog.phytools.org/2017/06/generating-set-of-random-re
> solutions-of.html.
>
> All the best, Liam
>
> Liam J. Revell, Associate 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 6/21/2017 11:02 AM, Liam J. Revell wrote:
>
>> [This sender failed our fraud detection checks and may not be who they
>> appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing]
>>
>>
>> Hi Laura.
>>
>> The phytools functions resolveNode and resolveAllNodes could be used.
>> They resolve either a single node in all possible ways; or all nodes in
>> all possible ways, returning a "multiPhylo" object. Note that in the
>> latter case the number of trees can be quite large. From the phytools
>> doc: "For resolveNode applied to a multifurcation with n descendants,
>> the number of resolved trees will be equal to the number of possible
>> rooted trees of n taxa. (For instance, three for a trifurcation, 15 for
>> a quadrifurcation, and so on.) For resolveAllNodes the number of fully
>> resolved trees will be equal to the product of numbers for resolveNode
>> applied to each multifurcation separately. (For instance, 45 for a tree
>> containing one trifurcation and one quadrifurcation.)" To get a random
>> set of resolved trees, rather than all possible trees (because this
>> number can be high), you could start with one multifurcating node in the
>> tree, resolve it in all ways using resolveNode, pick one of those
>> resolutions, then move to the next node & so on. I will try to post a
>> formal solution & then share it to the list.
>>
>> All the best, Liam
>>
>> Liam J. Revell, Associate 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 6/21/2017 10:38 AM, Laura Jackson wrote:
>>
>>> Hi all,
>>>
>>> I am using the ape package to randomly resolve polytomies using
>>> 'multi2di'
>>> and wondering if there is a way to use this function to get a single
>>> output
>>> tree file that contains multiple different randomly resolved trees using
>>> some number of resamplings?
>>>
>>> Thanks,
>>> -Laura
>>>
>>>
>> _______________________________________________
>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>> Searchable archive at
>> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>>
>

--
*Laura M. Jackson*
PhD Candidate
Department of Biology
185 Churchill Haines
University of South Dakota
414 E. Clark St.
Vermillion SD 57069-1746
Email: laura.jack...@usd.edu

[[alternative HTML version deleted]]

_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
```