[R-sig-phylo] Postdoc in PCM development in the Revell lab

2018-04-27 Thread Liam J. Revell 

Dear list.

I am advertising for a postdoctoral research position in my lab. The 
position is available more or less immediately.


This is a re-advertisement of a postdoc that I posted last year (but 
didn't fill) with two important updates, as follows:
1. The postdoc is for PCM development in particular, rather than 
phylogeny methods more broadly.
2. The postdoc is for a minimum 2 years (given satisfactory progress, 
etc.) rather than for one year as advertised previously.


I consider PCMs to include anything related to the use of phylogenies to 
make evolutionary inferences, rather than the estimation of phylogeny - 
but please contact me if you'd like clarification.


The deadline to apply is May 11. More information along with a link to 
apply is available on my blog: 
http://blog.phytools.org/2018/04/postdoc-to-work-on-pcm-development-in.html.


All the best, Liam

--
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/

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Re: [R-sig-phylo] grafting chronograms onto backbone phylogeny

2018-04-27 Thread Chris Law 
Thanks for the suggestions!

*Chris Law​ **|*
* ​*PhD Student
 *|*
* ​*University of California, Santa Cruz
​


Coastal Biology Building
​
130 McAllister Way
Santa Cruz, CA 95060
cj...@ucsc.edu *|* research.pbsci.ucsc.edu/eeb/cjlaw/
Small Mammal Research in the Forest Internship




On Thu, Apr 26, 2018 at 3:31 PM, Liam J. Revell  wrote:

> If your case is simple - like you have a tree with tips labeled by
> genus, and each species label from each subtree to be bound has tip
> labels in the format Genus_species, this could be done using bind.tree
> in ape.
>
> For instance:
>
> library(phytools)
> ## here's your backbone
> backbone<-read.tree(text="((A:2.0,B:2.0):1,C:3.0);")
> plotTree(backbone)
>
> ## here are your subtrees
> A<-read.tree(text="(A_sp1:1.0,A_sp2:1.0);")
> B<-read.tree(text="(B_sp1:1.5,B_sp2:1.5);")
> C<-read.tree(text="((C_sp1:0.5,C_sp2:0.5):0.5,C_sp3:1.0);")
> subtrees<-c(A,B,C)
>
> for(i in 1:length(subtrees)){
> genus<-strsplit(subtrees[[i]]$tip.label[[1]],"_")[[1]][1]
> h<-max(nodeHeights(subtrees[[i]]))
> tip<-which(backbone$tip.label==genus)
> backbone$edge.length[which(backbone$edge[,2]==tip)]<-
> backbone$edge.length[which(backbone$edge[,2]==tip)]-h
> backbone<-bind.tree(backbone,subtrees[[i]],where=tip)
> }
>
> plotTree(backbone)
>
> Something like that.
>
> (Of course you could also modify this so that you just manually identify
> the tips to bind to. Given the small size of your problem this is probably
> what you want.)
>
> All the best, Liam
>
> Liam J. Revell, Associate Professor of Biology
> University of Massachusetts Boston
> & Profesor Asociado, Programa de Biología
> Universidad del Rosario
> web: http://faculty.umb.edu/liam.revell/
>
> On 4/26/2018 4:19 PM, Brian O'Meara wrote:
>
>> Look at congruify.phylo in geiger (and the associated paper: Eastman
>> JM, LJ Harmon, and DC Tank. 2013. Congruification: support for time
>> scaling large phylogenetic trees. Methods in Ecology and Evolution).
>>
>> You could also look into SDM in ape (converting trees [not data] to
>> distance matrices, first): relevant paper Criscuolo, A., Berry, V.,
>> Douzery, E. J. P. , and Gascuel, O. (2006) SDM: A fast
>> distance-based approach for (super)tree building in phylogenomics.
>> Systematic Biology, 55, 740–755.
>>
>> Best, Brian
>>
>> ___
>>
>>
>> Brian O'Meara, http://www.brianomeara.info, especially Calendar
>
>> , CV <
>> http://brianomeara.info/cv/>, and Feedback > ing/feedback/>
>>
>> Associate Professor, Dept. of Ecology & Evolutionary Biology, UT
>> Knoxville Associate Head, Dept. of Ecology & Evolutionary Biology, UT
>> Knoxville Associate Director for Postdoctoral Activities, National
>> Institute for Mathematical & Biological Synthesis
>>  (NIMBioS)
>>
>>
>> On Thu, Apr 26, 2018 at 5:07 PM, Chris Law  wrote:
>>
>> Hi all,
>>>
>>> I am trying to graft 3 chronograms onto a family level backbone.
>>> Does anybody have any suggestions on what is the best way to do
>>> this? Or is going through the tree files in textwrangler the only
>>> way to do this.
>>>
>>> Thanks!
>>>
>>>
>>> *Chris Law​ **|* * ​*PhD Student *|* * ​*University of California,
>>> Santa Cruz ​
>>>
>>>
>>> Coastal Biology Building ​ 130 McAllister Way Santa Cruz, CA 95060
>>> cj...@ucsc.edu *|* research.pbsci.ucsc.edu/eeb/cjlaw/ Small Mammal
>>> Research in the Forest Internship >> u/envs/smurf>
>>>
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>>>
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