`Excellent. I have added those function to phytools on GitHub, so they`

`can be installed using devtools as follows:`

library(devtools) install_github("liamrevell/phytools")

Glad it was of help. - 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 11/2/2016 8:00 PM, Carlos Porto Filho wrote:

Thank you very much! That actually solved my problem. I couldn't express myself clearly but that was what I wanted.. that nodes with the same maximum path length to the tips should have the same height.. From a layman perspective that way to compute branch lengths is actually more logic for a tree representation format like newick (think of the number of outside parenthesis..) Thank you again! 2016-11-02 14:20 GMT-02:00 Liam J. Revell <liam.rev...@umb.edu <mailto:liam.rev...@umb.edu>>:Hi Carlos. After thinking about this, I realized that what you probably want isnot a node depth based on the number of nodes above that node - but the based on the maximum number of nodes separating that node from any leaf.I just posted a second solution for this on my blog here:http://blog.phytools.org/2016/11/modified-version-of-grafens-branch.html.Let me know if this is helpful. 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 <mailto:liam.rev...@umb.edu> blog: http://blog.phytools.org On 11/1/2016 10:32 PM, Liam J. Revell wrote:Hi Carlos. The edge lengths used for plotting (and thus the 'merge depths') are completely arbitrary when none are supplied. The algorithm used to compute the edge lengths is in the documentation for compute.brlen as follows: "Grafen's (1989) computation of branch lengths: each node is given a â€˜heightâ€™, namely the number of leaves of the subtree minus one, 0 for leaves. Each height is scaled so that root height is 1, and then raised at power 'rho' (> 0). Branch lengths are then computed as the difference between height of lower node and height of upper node." If you want to set it so that it is the number of descendant nodes, rather than leaves, that determines the height of each internal node, you could try something like the following: tree<-newickTree ndn<-function(tree,x){ dd<-c(Descendants(tree,x,"all"),x) sum(dd>Ntip(tree)) } nn<-1:(Ntip(tree)+tree$Nnode) h<-sapply(nn,ndn,tree=tree) edge.length<-vector() for(i in 1:nrow(tree$edge)) edge.length[i]<-diff(h[tree$edge[i,2:1]]) tree$edge.length<-edge.length plot(tree) 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 <mailto:liam.rev...@umb.edu> blog: http://blog.phytools.org On 11/1/2016 10:05 PM, Carlos Porto Filho wrote:Dear list, TL;DR: When I plot the newick tree ((((A,B),C,D),E),(((F,G),H),I)); shouldn't ((A,B),C,D) merge at the same level as ((F,G),H)? Or in a phylogenetic tree it doesn't matter? library(ape) newickTree <- read.tree(text="((((A,B),C),E),(((F,G),H),I));") plot(newickTree) goes just fine but then, when I add D: newickTree <- read.tree(text="((((A,B),C,D),E),(((F,G),H),I));") plot(newickTree) The merge between (A,B),C,D goes one level up (and consequently E too). Very long version: I'm developing my own hierarchical clustering algorithm that outputs a matrix like the one bellow: | Level 1 | Level 2 | Level 3 | Level 4 | Level 5|Level 6------------------------------------------------------------------------------------------------------1 | 1 | c(5,8) | c(2, 5, 8) | c(2, 5, 7, 8) | c(2, 5, 6, 7, 8) | 1:10 2 | 2 | c(5,8) | c(1, 5, 8) | c(2, 5, 7, 8) | c(2, 5, 6, 7, 8) | 1:10 3 | 3 | c(4,9) | c(3, 4, 9) | c(2, 5, 7, 8) | c(1, 2, 5, 7, 8) | 1:10 4 | 4 | c(4,9) | c(3, 4, 9) | c(3, 4, 9, 10) | c(2, 5, 6, 7, 8) | 1:10 5 | 5 | c(5,8) | c(1, 5, 8) | c(2, 5, 7, 8) | c(2, 5, 6, 7, 8) | 1:10 6 | 6 | c(5,8) | c(2, 5, 8) | c(2, 5, 7, 8) | c(1, 2, 5, 7, 8) | 1:10 7 | 7 | c(5,8) | c(2, 5, 8) | c(2, 5, 7, 8) | c(1, 2, 5, 7, 8) | 1:10 8 | 8 | c(5,8) | c(2, 5, 8) | c(2, 5, 7, 8) | c(2, 5, 6, 7, 8) | 1:10 9 | 9 | c(4,9) | c(3, 4, 9) | c(2, 5, 7, 8) | c(2, 5, 6, 7, 8) | 1:10 10| 10 | c(4,9) | c(3, 4, 9) | c(3, 4, 9, 10) | c(2, 5, 6, 7, 8) | 1:10 I want to plot a dendrogram based on this and the best idea I had was to convert that matrix to a newick tree format and use ape to read it and plot as a dendrogram. So the corresponding newick tree would be newickTree <- read.tree(text="(((((5,8),1,2),7),6),(((4,9),3),10));") plot(newickTree) But the levels are wrong.. I was expecting this: newickTree <-read.tree(text="(((((5:1,8:1):1,1:2,2:2):1,7:3):1,6:4):1,(((4:1,9:1):1,3:2):1,10:3):2);")plot(newickTree) I know that I can just specify the heights and solve my problem but that would make my code more complex. One idea I had reading the last thread (Making ultrametric trees) was to make every height = 1 and read it with chronos() newickTree <-read.tree(text="((((A:1,B:1):1,C:1,D:1):1,E:1):1,(((F:1,G:1):1,H:1):1,I:1):1);")dendr <- chronos(newickTree) plot(dendr) but it doesn't look right.. Sorry for the newbie questions.. I just wanted a way to make myalgorithmoutput a dendrogram. Thanks in advance.-- Carlos Porto Filho Bioengenharia - EESC / IQSC / FMRP - USP

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