phylogeny

Working with a phylogenetic tree in R, I would like to create a matrix which indicates if each branch of the tree (B1 to B8) is associated with each species (A to E), where 1s indicate that the branch is associated. (Shown below) The R function which.edge() is useful for identifying the terminal branch for a species. but it doesn't identify ALL the branches associated with each species. What function could I use to identify all the branches in the tree that go from the root to the tip for each species? Example Tree library(ape) ex.tree <- read.tree(text="(A:4,((B:1,C:1):2,(D:2,E:2):1):1);")

I have several thousand gene trees that I am trying to ready for analysis with codeml. The tree below is a typical example. What I want to do is automate the collapsing of tips or nodes that appear to be duplicates. For instance, descendants of node 56 are tips 26, 27, 28 etc all the way to 36. Now all of these other than tip 26 appear to be duplicates. How can I collapse them all into a single tip, leaving just tips 28 and one representative of the other tips as the descendants of node 56? I know how to manually do this one by one, but I am trying to automate the process so that a function

I'm trying to produce a non-ultrametric tree using the ape package in R and the function plot.phylo(). I'm struggling to find any documentation on how to keep the tip label vertically aligned on their left edge and with a series of dots (variable length) linking the species' name to the tip of the node. Any help would be much appreciated as well as links to other packages within R that may be able to achieve this. An example of the newick tree I don't have any tree examples of what i want, however, the description seems self explanatory. the labels would all be shifted to the very right, and