Numerous phylogenetic methods have been proposed, because no single method performs well in all situations. There are three types of methods: distance matrix , maximum parsimony, and maximum likelihood. In distance matrix methods, the number of nucleotide or amino acid substitutions between sequences is treated as a distance and computed for all pairs of taxa. The phylogenetic tree is constructed based on these distances. We will not spend time on the distance methods but instead focus on maximum parsimony and maximum likelihood.