Many methods exist for the construction of such trees.
I have developed procedures for building phylogenetic trees using information on the aligned sequences of four species at a time. I then build an overall phylogenetic tree by fitting together the trees for each quartet. Several methods may be used to compute the tree for each quartet. The most common methods are maximum parsimony, maximum likelihood, or neighbor-joining. I have also developed a new method called Higher Order Parsimony, which introduces corrections to maximum parsimony calculations and thereby reduces the effects of long-branch attraction.