New Approaches for Analyzing Biological Sequences

We developed new approaches for analyzing biological sequences, a fundamental task in modern molecular biology. First, we formulated and analyzed heuristics for detecting new memebers of gene famiies using judicious primer selection in polymerase chain reactions. Secondly, we focused on reliability aspects of phylogenetic tree reconstruction and developed methods that detect trees with near-optimal cost yet diverse topologies. Finally, we investigated general approaches for assessing the topographical similarity between phylogenetic solution spaces induced by various optimality criteria.