Quality criteria of genetic algorithms for construction of phylogenetic trees

In this article the suitability of two different tree representations for t he construction of phylogenetic trees with genetic algorithms is examined. On the one hand tree topologies are represented by means of a distance matr ix while on the other hand the Prufer number tree representation is used. T o assess the adequacy of both approaches a set of recently proposed quality criteria is used. The quality criteria can be used to monitor genetic algo rithm approaches differing in configuration and setup, fitness function, or representation. In addition to the criteria for the repeatability of the o ptimization, criteria for the coverage of the search space are also used. O n the basis of the optimization results of simulated data, the quality crit eria show, in contrast to the error plots, a clear difference in the effici ency of both representations. It is concluded that the Prufer number repres entation yields a diverse set of good quality topologies while the distance matrix representation mainly returns the optimal topology. (C) 1999 John W iley & Sons, Inc.