Reconstruction of the evolutionary history of genes and species is currently one of the most important subjects in molecular evolution. If reliable phylogenies are produced, they will shed light on the sequence of evolutionary events that generated the present day diversity of genes and species and help us to understand the mechanisms of evolution as well as the history of organisms.
Phylogenetic relationships of genes or organisms usually are presented in a treelike form with a root, which is called a rooted tree. It also is possible to draw a tree without a root, which is called an unrooted tree. The branching pattern of a tree is called a topology.
There are numerous methods for constructing phylogenetic trees from molecular data (Nei and Kumar 2000). They can be classified into Distance methods, Parsimony methods, and Likelihood methods. These methods are explained in Swofford et al. 1996, Li (1997), Page and Holmes (1998), and Nei and Kumar (2000).