Despite recent advances achieved by application of high-performance computing methods
and novel algorithmic techniques to maximum likelihood (ML)-based inference programs …

Delineating the tremendous growth in this area, the Handbook of Approximation Algorithms
and Metaheuristics covers fundamental, theoretical topics as well as advanced, practical …

Hannenhalli and Pevzner gave the first polynomial-time algorithm for computing the
inversion distance between two signed permutations, as part of the larger task of …

Untitled Page 1 Page 2 Natural Computing Series Series Editors: G. Rozenberg Th.Bäck AEEiben
JNKok HPSpaink Leiden Center for Natural Computing AdvisoryBoard: S.Amari G.Brassard …

The enormous complexity of biological systems at the molecular level must be answered
with powerful computational methods. Computational biology is a young field, but has seen …

In this paper we present a profiling methodology and toolkit for helping developers discover
hidden asymptotic inefficiencies in the code. From one or more runs of a program, our …

There are two approaches to automatically deriving symbolic worst-case resource bounds
for programs: static analysis of the source code and data-driven analysis of cost …

We report on new techniques we have developed for reconstructing phylogenies on whole
genomes. Our mathematical techniques include new polynomial-time methods for bounding …

Phytogenies derived from gene order data may prove crucial in answering some
fundamental open questions in biomolecular evolution. Yet very few techniques are …

Phylogenetic trees are commonly reconstructed based on hard optimization problems such
as maximum parsimony (MP) and maximum likelihood (ML). Conventional MP heuristics for …