Phylogenetic search is a key tool used in a variety of biological research endeavours. However, this search problem is known to be computationally difficult, due to the astronomically large search space, making the use of heuristic methods necessary. The performance of heuristic methods for finding Maximum Likelihood (ML) trees can be improved by using parsimony as an initial estimator for ML. ...

In this paper, we investigate a conjecture by Arndt von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This conjecture deals with the question whether Maximum Parsimony trees are hereditary. The conjecture suggests that a Maximum Parsimony tree for a particula...

Bloat control is an important aspect of evolutionary computation methods, such as genetic programming, which must deal with genomes of arbitrary size. We introduce three new methods for bloat control: Biased Multi-Objective Parsimony Pressure (BMOPP), the Waiting Room, and Death by Size. These methods are unusual approaches to bloat control, and are not only useful in various circumstances, but...

An assignment of colors to objects induces a natural integer weight on each tree that has these objects as leaves. This weight is called “parsimony length” in biostatistics and is the basis of the “maximum parsimony” technique for reconstructing evolutionary trees. Equations for the average value (over all binary trees) of the parsimony length of both fixed and random colorations are derived us...