Abstract A tree is nonreticulated network, and there are rooted (with the location of the common ancestor) and unrooted trees. If we have an appropriate outgroup node (operational taxonomic unit (OTU)) in one unrooted tree, we can transform this to rooted tree. By this way, any unrooted tree can have the one-to-one correspondence. The number of possible unrooted trees rapidly increases as the number of OTUs increases. If the rate of evolution is constant, or if the molecular clock exists, we can obtain a rooted tree with branch lengths proportional to evolutionary time. We have to be careful to estimate a species tree from gene trees, for there are many uncertainties in speciation.