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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>>>
>>> ___ R-sig-phylo mailing
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>>> istinfo/r-sig-phylo Searchable
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>>>
>>>
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>>
>>

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

2018-04-26 Thread Liam J. Revell 

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 
, and 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 



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

2018-04-26 Thread Brian O'Meara 
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
, and 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
> 
>
> [[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-ph...@r-project.org/
>

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

2018-04-26 Thread Chris Law 
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


[[alternative HTML version deleted]]

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