UPGMA

This method assumes that the rate of nucleotide or amino acid substitution is the same for all evolutionary lineages. An interesting aspect of this method is that it produces a tree that mimics a species tree, with the branch A branch is a line connecting either two internal nodes to each other or an external node to an internal node in a phylogenetic tree. The length of a branch denotes the genetic distance (e.g., number of substitutions per unit time) between the two taxa it connects. lengths for two OTUs being the same after their separation.  Because of the assumption of a constant rate of evolution, this method produces a rooted tree A rooted tree is one in which the root of the phylogenetic tree is determined by using the mid-point rooting or out-group sequences., though it is possible to remove the root for certain purposes. The algorithm for UPGMA is discussed in detail in Nei and Kumar (2000Nei_and_Kumar_2000, page 87).