In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus, inferring trees from molecular data was shown to be NP-hard. This causes problems, if large data sets are used. This review gives an introduction to molecular phylogenetic methods and to the problems biologists are facing in molecular phylogenetic analyses.

12 pages including 4 figs., for Computing in Science and Engineering (Review), abstract change, 1 paragraph changed in section 5 and 1 reference added, correction of Fig. 3 (text moved away from arrow), modification of conclusions