Hi Liam
Thank you very much for your input. I am working with host and parasite trees.
The host tree topology looks like:
TREE HOST =
((((H4,H5)H3,H6)H2,((H9,(H11,H12)H10)H8,(H14,((H17,H18)H16,H19)H15)H13)H7)H1,(H21,H22)H20)H0;
and the heights above the root are given as
[RANKS represents the ranks of the nodes in the tree]
[Syntax is: nodename timezone_from timezone_to]
RANKS
H0 2 2,
H1 4 4,
H2 5 5,
H3 6 6,
H4 15 15,
H5 15 15,
H6 15 15,
H7 7 7,
H8 9 9,
H9 15 15,
H10 10 10,
H11 15 15,
H12 15 15,
H13 8 8,
H14 15 15,
H15 11 11,
H16 15 15,
H17 15 15,
H18 15 15,
H19 15 15,
H20 3 3,
H21 15 15,
H22 15 15,
Thanks again for your time.
Juan
> 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 <http://www.uv.es/%7Ebalbuena>
> > P.O. Box 22085
> > http://www.uv.es/cophylpaco <http://www.uv.es/cavanilles/zoomarin/indexhtm>
> > 46071 Valencia, Spain
> > e-mail: j.a.balbu...@uv.es <mailto:j.a.balbu...@uv.es> tel. +34 963
> > 543 658 fax +34 963 543 733
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> >
> >
> >
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>
--
--
Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary
Biology
University of Valencia
P.O. Box 22085
46071 Valencia, Spain
e-mail: j.a.balbu...@uv.es tel. +34 963 543 658
+++++++++++++++++++++++++++++++++++++++++++++++++++
NOTE! For shipments by EXPRESS COURIER use the
following street address:
C/ Catedrático José Beltrán 2, 46980 Paterna
(Valencia), Spain.
+++++++++++++++++++++++++++++++++++++++++++++++++++
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