rgenetree
(Package: HyPhy) :
Samples gene family trees that evolved on a species tree with various conditions.
Samples gene family trees that evolved on the branches of a species tree under the birth-death process. Trees may be conditioned on various priors for the number of reconstructed gene lineages at the root of the species tree, on the total number of genes in the gene tree, on the number of genes in each tip of the species tree, on at least one gene in each tip of the species tree or some combination of those conditions.
requiprobable
(Package: HyPhy) :
Sample trees from an equiprobable labeled, semi-labeled or unlabeled distribution
An equiprobable distribution assumes that all tree topologies are equally likely. The degree of tip labeling affects the number of possible tree topologies. In labeled trees all the tips are different, in unlabeled trees all the tips are the same and in semi-labeled trees the tips fall into groups in which any individual tip may or may not be the same as any other.
HyPhy-package
(Package: HyPhy) :
Macroevolutionary phylogentic analysis of species trees and gene trees
A Bay Area high level phylogenetic analysis package mostly using the birth-death process. Analysis of species tree branching times and simulation of species trees under a number of different time variable birth-death processes. Analysis of gene tree species tree reconciliations and simulations of gene trees in species trees under the birth-death process.
providing 
.