Dear Lev,
I simple way to do what you request would be to follow this example with
your data:
> library(ape)
# here I'm creating a random tree with branch lengths
> treeBL <- rtree(10)
> treeBL$edge.length
[1] 0.59962263 0.76458987 0.48171189 0.26387301 0.76967429 0.42754456
[7] 0.30173612 0.10535179 0.01769042 0.49671428 0.61575421 0.91297819
[13] 0.52992782 0.68690369 0.35537999 0.56974770 0.97019530 0.49849792
# this would be the tree with the same topology but without branch lengths
> treeNN <- treeBL
> treeNN$edge.length <- NULL
> treeNN
Phylogenetic tree with 10 tips and 9 internal nodes.
Tip labels:
t1, t9, t4, t3, t7, t10, ...
Rooted; no branch lengths.
# create node labels
> treeNN$Nnode
[1] 9
> treeNN$node.label <- paste("n",1:treeNN$Nnode,sep='')
> treeNN$node.label
[1] "n1" "n2" "n3" "n4" "n5" "n6" "n7" "n8" "n9"
> treeNN
Phylogenetic tree with 10 tips and 9 internal nodes.
Tip labels:
t1, t9, t4, t3, t7, t10, ...
Node labels:
n1, n2, n3, n4, n5, n6, ...
Rooted; no branch lengths.
# check if the internal structure of both trees is identical
> identical(treeNN$edge,treeBL$edge)
[1] TRUE
> if (identical(treeNN$edge,treeBL$edge)){
+ newtree <- treeBL
+ newtree$node.label <- treeNN$node.label
}
> newtree
Phylogenetic tree with 10 tips and 9 internal nodes.
Tip labels:
t1, t9, t4, t3, t7, t10, ...
Node labels:
n1, n2, n3, n4, n5, n6, ...
Rooted; includes branch lengths.
Hope this helps.
Cheers,
Santiago
--
Santiago Sánchez-Ramírez
Environmental Genomics Group
Max Planck Institute for Evolutionary Biology
August-Thienemann-Str. 2
24306 Plön
Germany
Website: https://sites.google.com/site/santiagosnchezrmirez/
>
> Message: 1
> Date: Wed, 13 Jan 2016 23:39:21 +0000
> From: "Yampolsky, Lev" <yampo...@mail.etsu.edu>
> To: Emmanuel Paradis <emmanuel.para...@ird.fr>, "Liam J. Revell"
> <liam.rev...@umb.edu>, Dan Rabosky <drabo...@umich.edu>
> Cc: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org>
> Subject: Re: [R-sig-phylo] getBtimes vs. branching.times
> Message-ID: <d2bc4988.7376e%yampo...@mail.etsu.edu>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Colleagues,
>
> Thank you very much for your help, it?s all clear now. (I got way more
> than I asked for, for example, my trees include only extant taxa). And
> yes, branching.times() and getBtimes() return exact same numbers of
> course, I just didn?t understand ow indexing works.
>
> Next question, a very simple one again.
>
> I have two newick trees, identical topology. In one I have branch lengths,
> in the other I have node names. I would like a tree with both. How do I do
> this?
>
> Thanks in advance!
>
> --
> Lev Yampolsky
>
> Professor
> Department of Biological Sciences
> East Tennessee State University
> Box 70703
> Johnson City TN 37614-1710
> Cell 423-676-7489
> Office/lab 423-439-4359
> Fax 423-439-5958
>
>
>
>
>
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