Phylogenetic Hypotheses and the Utility of Multiple Sequence Alignment

Abstract

Multiple sequence alignment (MSA) is a potentially useful technique in phylogenetic analysis. This chapter examines the relative effectiveness of MSA and constructs and evaluates phylogenetic hypotheses without the use of this technique, first defining phylogenetic hypothesis, the problem, and the criteria used to assay the relative merits of hypotheses. It also defines the meaning of the utility of a technique, compares the results of alternate techniques, and criticizes the traditional approach to alignment and phylogenetic analysis, with a specific implementation of simultaneous phylogeny and alignment construction. The final section compares the results of a “one-step” optimization heuristic embodied in POY4 with the MSA + Search approach embodied by Clustal, using a large number of small data set simulations run under a variety of conditions and a few larger real data sets.