Question

Describe maximum parsimony.

Answer 1

Maximum Thrift is a method / philosophy that considers the shortest tree (in number of transformation steps) the best hypothesis about the phylogenetic relationship of a given set of terminals. Transformation step is the cost attributed to the change of character state in a given branch of the tree, be it the change from one nucleotide base to another, amino acids, or the color of an animal's iris. The fewer transformations, the shorter the tree, and therefore the more parsimonious.  In this method, what programs do is to investigate as many alternative topologies as possible (or all if their array has less than 25 terminals; see more details below) given their character array. Each will be measured, and the shorter (optimal) trees will be retained as the most parsimonious result.