Phylogenetic trees (or phylogenies) may be loaded and stored within PASSaGE; their usefulness is limited at this time but is expected to grow in the future. Like the tessellation matrices, phylogenetic trees have a special internal format, but unlike the tessellation matrices, phylogenies can easily be imported into and exported from PASSaGE. Phylogenies in PASSaGE include not only the topology (branching pattern), but also branch lengths and terminal (tip) labels. In PASSaGE, phylogenies do not have to be bifurcating (i.e., polytomies are allowable), but they are intrinsically rooted (unrooted trees can be faked using zero length branches at the base of the tree).