Hey Andy, Simulating the bifurcation times in a tree with n extant species and age t (where t is either mrca or the origin of the first species), assuming constant speciation and extinction rates (and possibly a sampling probability rho), can be done within the R package TreeSim using the function: sim.bd.taxa.age
Note: the output is a tree with branch length. Therefore, use branching.times(tree) for obtaining the bifurcation times. These bifurcation times can be put on your constrained tree topology in the following: 1) "sort" (or "rank") the interior nodes in your tree where each sorting is equally likely (the resulting tree is called ranked tree, see eg Semple&Steel Phylogenetics 2003. For sorting the nodes uniformly at random, you can use the shuffle idea introduced in Ford, Matsen, Stadler 2009 Syst Biol). 2) Then the i-th largest branching time is put on the i-th node in your tree. 1-2) works as ranked tree and branching time distribution are independent under the birth-death process and each ranked tree has equal probability. Simulating 1) is fairly easy with this shuffle concept, if you have questions or need help, let me know! Best Tanja Stadler _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
