Define a phylogenetic tree Hy-Phy uses standard (Newick) tree definitions. Thus, the statement Tree myTree = (((a,b),c),d); defines a tree named myTree with four OTUs, or taxa, named a, b, c, and d. In this case, the names correspond to the names in the Hy-Phy batchfile. While this is not necessary, it is strongly recommended to avoid confusion. Hy-Phy will accept either rooted or unrooted trees; however, for most purposes rooted trees are automatically unrooted by Hy-Phy because likelihood values for unrooted trees are the same as those for rooted trees. The Hy-Phy Tree data structure is much more complex than simply describing a tree topology. The Tree variable includes both topology information, as well as evolutionary model information. The default behavior of a Tree statement is to attach the most recently defined Model to all branches in the tree. Thus, it is critical that the Model statement appears before the Tree statement. We will discuss more advanced uses of the Tree statement later.
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002