Phylogenetics is the study of
evolutionary relationships. Phylogenetic analysis is the means of inferring or
estimating these relationship. The evolutionary history inferred from
phylogenetic analysis is usually depicted as branching (treelike) diagrams,
which represent a ort of pedigree of the inherited relationships among
molecules (“gene trees”), organisms, or both. The four steps in phylogenetic
analysis of DNA sequences are alignment, determining the substitution model,
tree building, and tree evaluation. While other scientific analysis generally
have empirical bases, phylogenetic analysis do not. The
physical events yielding a phylogeny happened in the past, and can only be
inferred or estimated.
The three major tree-building criteria are distance, maximum parsimony, and
maximum likelihood.