Fast character optimization in parsimony phylogeny reconstruction

The problem of finding a phylogeny with maximum parsimony is one of the main problems in computational biology. While it is impossible to search the possible tree space exhaustively for large data sets, most heuristic approaches try to search in the neighborhood of sub-optimal trees. The speed of computing a score for each tree (e.g. tree length or total number of character changes) is as important as the different tree search strategies. Some techniques include short-cuts that have not been proven to be exact, and an incremental character optimization approach by which the speedup gains depends on data sets and is hardly analyzed in theory. This paper describes an exact and fast algorithm to compute tree length and our algorithm can obtain great speedup for any data sets. We discuss the algorithm for Fitch-parsimony, but it can also be applied to Wagner-parsimony.