Re: [R-sig-phylo] phylogenetic signal different from BM and random

[Theodore Garland]

Dear Florian,

What do you mean, exactly?  Do you mean the K statistics is, say, about
0.5, and that the randomizaton test for phylogenetic signal (Blomberg et
al. 2003), which is based on the MSE not K, is significant, indicating that
you do have some degree of signal (more than zero)?

Cheers,
Ted

Theodore Garland, Jr., Distinguished Professor

Department of Biology

University of California, Riverside

Riverside, CA 92521

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On Wed, Nov 30, 2016 at 8:50 AM, Menzel, Dr. Florian 
wrote:

> Dear all,
>
> I am analysing phylogenetic signal using Blomberg's K. For several of my
> traits (univariate, continuous), the signal strongly deviates both from
> random and from the Brownian Motion.
>
>
> I am unsure how to interpret this. Can you give me some advice what this
> could mean?
>
>
> Thanks a lot!
>
>
> Florian
>
>
> Dr. Florian Menzel
> Department of Evolutionary Biology, Institute of Zoology
> University of Mainz
> Johannes-von-Müller-Weg 6
> 55128 Mainz, Germany
> phone: 0049-6131-3927848
> http://www.bio.uni-mainz.de/zoo/evobio/73_ENG_HTML.php
>
> Gemeinsam einen Unterschied machen!
> www.synagieren.de
>
> 'For every complex problem there is an answer that is clear, simple, and
> wrong.' (Henry Louis Mencken)
>
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>
>
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>

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Re: [R-sig-phylo] get branch lengths from distances to root

[Cecile Ane]

One way would be to label the root to make it a leaf, and apply NJ.
Neighbor-joining reconstructs the original branch lengths (and topology) given 
tree-distances between the leaves.
Cécile

On Nov 30, 2016, at 10:30 AM, Juan Antonio Balbuena 
> wrote:


Hi all

This is a simple question:

I have a set of ultrametric trees with information on their topology but 
without branch lengths. On a separate file, I have the distances of each node 
and leaf to the root. Can someone instruct me on how to to compute the branch 
lengths of the tree with these two separate bits of information?

Many thanks in advance

Juan A. Balbuena

--
Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
University of Valencia
http://www.uv.es/~balbuena
P.O. Box 22085
http://www.uv.es/cophylpaco
46071 Valencia, Spain
e-mail: j.a.balbu...@uv.estel. +34 963 543 658   
 fax +34 963 543 733

NOTE! For shipments by EXPRESS COURIER use the following street address:
C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain.

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[R-sig-phylo] get branch lengths from distances to root

[Juan Antonio Balbuena]

  
  
Hi all
This is a simple question:
I have a set of ultrametric trees with information on their
  topology but without branch lengths. On a separate file, I have
  the distances of each node and leaf to the root. Can someone
  instruct me on how to to compute the branch lengths of the tree
  with these two separate bits of information?
Many thanks in advance
Juan A. Balbuena


-- 
  
  

  Dr.
Juan
A. Balbuena 
Cavanilles Institute of Biodiversity and Evolutionary
Biology 
University of
Valencia           
           
           
        http://www.uv.es/~balbuena

P.O. Box
22085           
           
           
           
    http://www.uv.es/cophylpaco
46071 Valencia,
Spain

e-mail: j.a.balbu...@uv.es   
tel.
+34 963 543 658    fax +34 963 543 733 
 
NOTE! For shipments by EXPRESS COURIER use
  the following street
  address: 
  C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia),
  Spain. 
  
  

  


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Re: [R-sig-phylo] get branch lengths from distances to root

[Liam J. Revell]

Hola Juan.

If your heights (distances) above the root are a vector h in the order 
of the node indices of the tree (in tree$edge) it would be as easy as:


tree$edge.length<-rep(NA,nrow(tree$edge))
for(i in 1:nrow(tree$edge))
tree$edge.length[i]<-h[tree$edge[i,2]]-h[tree$edge[i,1]]

If it the nodes are labeled in a different fashion, then it would be 
slightly more complicated (for instance, involving the identifying MRCAs 
or matching nodes), but similar. How are your node & leaf heights organized?


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 11/30/2016 11:30 AM, Juan Antonio Balbuena wrote:

Hi all

This is a simple question:

I have a set of ultrametric trees with information on their topology but
without branch lengths. On a separate file, I have the distances of each
node and leaf to the root. Can someone instruct me on how to to compute
the branch lengths of the tree with these two separate bits of information?

Many thanks in advance

Juan A. Balbuena


--

Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
University of Valencia
http://www.uv.es/~balbuena 
P.O. Box 22085
http://www.uv.es/cophylpaco 
46071 Valencia, Spain
e-mail: j.a.balbu...@uv.es tel. +34 963
543 658fax +34 963 543 733

*NOTE!*For shipments by EXPRESS COURIER use the following street address:
C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain.




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