PAUP 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees, for use in Macintosh, UNIX/UMS or DOS-based formats. The use of high-speed computer analysis of molecular, morphological and/or behavioural data to infer phylogenetic relationships has expanded well beyond its central role in evolutionary biology, to encompass applications as diverse as conservation biology, ecology and forensic studies. The success of previous versions of PAUP: Phylogenetic Analysis Using Parsimony has made it the most widely used software package for the inference of evolutionary trees. In addition, the PAUP manual has proved to be an essential guide, serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well as an important reference for experts in the field. With the inclusion of maximum likelihood and distance methods in PAUP 4.0, the new version represents a great improvement over its predecessors. The speed of the branch-and-bound algorithm has also been enhanced and a number of new features have been added, from agreement subtrees to tests for combinability of data and permutation tests for nonrandomness of data structure.

These, together with many other improvements, will make PAUP 4.0 an even more indispensable tool in comparative biological analysis. PAUP 4.0 and MacClade use a common data file format (NEXUS), allowing easy interchange of data between the two programs.