ABSTRACT
Data analysis in phylogenomics has two dimensions: whether characters or distances are used, and whether an algorithm or an optimality criterion is used. Character states in molecular data may include the presence or absence of genes and the sequence states of nucleotides or amino acids, and these can be weighted relative to each other. Characters themselves can be weighted relative to one another. Maximum parsimony analysis is a character-based method that attempts to minimize the number of evolutionary character-state changes on a particular tree topology by use of a mathematical optimality criterion. It is based on the well-known principle of Occam’s razor. Fitch’s algorithm is a central tool in maximum parsimony, and it uses set theory.
