TOWARDS INTEGRATION OF MULTIPLE ALIGNMENT AND PHYLOGENETIC TREE CONSTRUCTION

A central problem in the study of molecular evolution is the reconstru ction of the history of a set of biological sequences in the form of a phylogenetic tree. One step in calculating this tree is the computati on of a multiple alignment. Most existing approaches treat the two pro blems of multiple alignment and tree construction as separate while in fact they influence each other. Based on three-way alignments of pre- aligned groups of sequences we adapt a commonly used tree construction procedure to produce both tree and multiple alignment simultaneously. In contrast to existing iterative algorithms the new method can chang e alignments made early in the course of the computation at a later st age. A sufficient criterion to prevent the introduction of edges with negative length reduces the number of three-way alignments that need t o be computed, Applications of the new approach to the alignment of pr otein and of nucleic acid sequences are presented.