Quadratic Assignment Problem. 1 Acknowledgments

When they introduced the Ant System paradigm, Dorigo, Maniezzo, and Colorni also suggested an improvement to the original algorithm. By making use of global information, a set of ‘elitist ’ ants could focus the search, potentially accelerating convergence on an optimal solution. In a later paper, White, Kaegi, and Oda proposed a refinement of elitism in which local information is used instead of global information. By focusing the search on the local best tours (LBT) rather than the global best tour, the ants could search a wider area and avoid becoming trapped in local optima. Test results using the symmetric Travelling Salesman Problem showed considerable promise. We will examine the effectiveness of this refinement when applied against the assymetrica

Toward automatic reconstruction of a highly resolved tree of life.

We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor