Phylogenetics in R: obtaining internal branch lengths

Question

[spiral01]

I am currently using the ape package function read.tree to read in several thousand newick format trees into R. An example tree is:

((Anopheles_christyi:0.057946,Anopheles_epiroticus:0.076668):0.009683,((((Anopheles_arabiensis:0.005646,Anopheles_melas:0.00841):0.001469,Anopheles_quadriannulatus:0.006608):0.002261,(Anopheles_gambiae:0.000492,Anopheles_coluzzii:0.039824):0.010745):0.005868,Anopheles_merus:0.02839):0.083449):1.546411;

I am trying to remove trees that have several internal branches of short length but my problem is that these branch lengths do not transfer into r when I read the trees in. I can obtain edge lengths using: treelist[[1]]$edge.length but this ofcourse does not give me the internal branch lengths that I require. Here is the output:

[1] 0.086351 0.083449 0.005868 0.002261 0.001469 0.005646 0.008410 0.006608 0.010745
[10] 0.000492 0.039824 0.028390

So what I am asking is that is there a way of identifying internal branch lengths in R, and if not is there another package anyone could recommend to do this?

[Jean-Karim Heriche]

tree$edge.list gives the length of all branches, including internal ones. Is the problem that your example output of $edge.list doesn't match the values from your example tree ? In that case, I would suspect some tree formating issue. Reading your example tree with read.tree(), tree$edge.length gives me:

[1] 0.009683 0.057946 0.076668 0.083449 0.005868 0.002261 0.001469 0.005646 0.008410 0.006608 [11] 0.010745 0.000492 0.039824 0.028390

Answer 1

[Klaus S]

If you would have looked in the help of read.tree, you will find:

...

Value

an object of class "phylo" with the following components:

edge

a two-column matrix of mode numeric where each row represents an edge of the tree; the nodes and the tips are symbolized with numbers; the tips are numbered 1, 2, ..., and the nodes are numbered after the tips. For each row, the first column gives the ancestor.

...

so

tree$edge.length[tree$edge[,2] > Ntip(tree)]

gives you the edge length of the internal edges.