Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima


  • Pablo A. Goloboff

    1. Consejo Nacional de Investigaciones Cientificas y Técnicas, Instituto Miguel Lillo, Miguel Lillo 205, 4000 S. M. de Tucumn, Argentina
    Search for more papers by this author


New methods for parsimony analysis of large data sets are presented. The new methods are sectorial searches, tree-drifting, and tree-fusing. For Chase et al.'s 500-taxon data set these methods (on a 266-MHz Pentium II) find a shortest tree in less than 10 min (i.e., over 15,000 times faster than PAUP and 1000 times faster than PAUP*). Making a complete parsimony analysis requires hitting minimum length several times independently, but not necessarily all “islands” for Chase et al.'s data set, this can be done in 4 to 6 h. The new methods also perform well in other cases analyzed (which range from 170 to 854 taxa).