I didn't see the email that this addresses, but I will add a couple of comments to Juan's suggestion:
(1) phytools::cophylo does not require the input trees to have branch lengths. If they do not, arbitrary branch lengths for plotting are computed using ape::compute.brlen. (2) The code suggested by Juan does indeed assign branch lengths to the tree; however, it has effect of assigning different depths for equivalently nested relationships. If you don't like the spacing of compute.brlen, it is possible to change it using the argument 'power.' 0<power<1 results in divergences between sister taxa pushed backward in time & may look better than the default. All the best, Liam Liam J. Revell Associate Professor, University of Massachusetts Boston Profesor Asistente, Universidad Católica de la Ssma Concepción web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org On 12/12/2018 12:07 PM, Juan Antonio Balbuena wrote: > You can try this: > > tree<- compute.brtime(tree, tree$Nnode:1) > > It will produce an ultrametric tree with its nodes well separated. > > I hope it helps > > All the best > _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
