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 determining the shortest sequence of inversions needed to transform one permutation into the other. Their algorithm (restricted to distance calculation) proceeds in two stages: in the first stage, the overlap graph induced by the permutation is decomposed into connected components; then, in the second stage, certain graph structures (hurdles and others) are identified. Berman and Hannenhalli avoided the explicit computation of the overlap graph and gave an O(n alpha(n)) algorithm, based on a Union-Find structure, to find its connected components, where a is the inverse Ackerman function. Since for all practical purposes alpha(n) is a constant no larger than four, this algorithm has been the fastest practical algorithm to date. In this paper, we present a new linear-time algorithm for computing the connected components, which is more efficient than that of Berman and Hannenhalli in both theory and practice. Our algorithm uses only a stack and is very easy to implement. We give the results of computational experiments over a large range of permutation pairs produced through simulated evolution; our experiments show a speed-up by a factor of 2 to 5 in the computation of the connected components and by a factor of 1.3 to 2 in the overall distance computation.

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Phylogenies (that is, tree-of-life relationships) derived from gene order data may prove crucial in answering some fundamental open questions in biomolecular evolution. Real-world interest is strong in determining these relationships. For example, pharmaceutical companies may use phylogeny reconstruction in drug discovery for finding plants with similar gene production. Health organizations study the evolution and spread of viruses such as HIV to gain understanding of future outbreaks. And governments are interested in aiding the production of foodstuffs like rice, wheat, and corn, by understanding the genetic code. Yet very few techniques are available for such phylogenetic reconstructions. Appropriate tools for analyzing such data may help resolve some difficult phylogenetic reconstruction problems; indeed, this new source of data has been embraced by many biologists in their phylogenetic work. With the rapid accumulation of whole genome sequences for a wide diversity of taxa, phylogenetic reconstruction based on changes in gene order and gene content is showing promise, particularly for resolving deep (i.e., old) branches. However, reconstruction from gene-order data is even more computationally intensive than reconstruction from sequence data, particularly in groups with large numbers of genes and highly rearranged genomes. We have developed a software suite, GRAPPA, that extends the breakpoint analysis (BPAnalysis) method of Sankoff and Blanchette while running much faster: in a recent analysis of a collection of chloroplast data for species of Campanulaceae on a 512-processor Linux supercluster with Myrinet, we achieved a one-million-fold speedup over BPAnalysis. GRAPPA currently can use either breakpoint or inversion distance (computed exactly) for its computati...

The ability to provide uniform shared-memory access to a significant number of processors in a single SMP node brings us much closer to the ideal PRAM parallel computer. In this paper, we develop new techniques for designing a uniform shared-memory algorithm from a PRAM algorithm and present the results of an extensive experimental study demonstrating that the resulting programs scale nearly linearly across a significant range of processors (from 1 to 64) and across the entire range of instance sizes tested. This linear speedup with the number of processors is, to our knowledge, the first ever attained in practice for intricate combinatorial problems. The example we present in detail here is a graph decomposition algorithm that also requires the computation of a spanning tree; this problem is not only of interest in its own right, but is representative of a large class of irregular combinatorial problems that have simple and efficient sequential implementations and fast PRAM algorithms, but have no known efficient parallel implementations. Our results thus offer promise for bridging the gap between the theory and practice of shared-memory parallel algorithms.

A phylogeny is the evolutionary history of a group of organisms; systematists (and other biologists) attempt to reconstruct this history from various forms of data about contemporary organisms. Phylogeny reconstruction is a crucial step in the understanding of evolution as well as an important tool in biological, pharmaceutical, and medical research. Phylogeny reconstruction from molecular data is very difficult: almost all optimization models give rise to NP-hard (and thus computationally intractable) problems. Yet approximations must be of very high quality in order to avoid outright biological nonsense. Thus many biologists have been willing to run farms of processors for many months in order to analyze just one dataset. High-performance algorithm engineering offers a battery of tools that can reduce, sometimes spectacularly, the running time of existing phylogenetic algorithms, as well as help designers produce better algorithms. We present an overview of algorithm engineering techniques, illustrating them with an application to the "breakpoint analysis" method of Sankoff et al., which resulted in the GRAPPA software suite. GRAPPA demonstrated a speedup in running time by over eight orders of magnitude over the original implementation on a variety of real and simulated datasets. We show how these algorithmic engineering techniques are directly applicable to a large variety of challenging combinatorial problems in computational biology.

Many large-scale phylogenetic reconstruction methods attempt to solve hard optimization problems (such as Maximum Parsimony (MP) and Maximum Likelihood (ML)), but they are severely limited by the number of taxa that they can handle in a reasonable time frame. A standard heuristic approach to this problem is the divide-and-conquer strategy: decompose the dataset into smaller subsets, solve the subsets (i.e., use MP or ML on each subset to obtain trees), then combine the solutions to the subsets into a solution to the original dataset. This last step, combining given trees into a single tree, is known as supertree construction in computational phylogenetics. The traditional application of supertree methods is to combine existing, published phylogenies into a single phylogeny. Here, we study supertree construction in the context of divide-and-conquer methods for large-scale tree reconstruction. We study several divide-and-conquer approaches and experimentally demonstrate their advantage over Matrix Representation Parsimony (MRP), a traditional supertree technique, and over global heuristics such as the parsimony ratchet. On the ten large biological datasets under investigation, our study shows that the techniques used for dividing the dataset into subproblems as well as those used for merging them into a single solution strongly influence the quality of the supertree construction. In most cases, our merging technique—the Strict Consensus Merger (SCM)—outperforms MRP with respect to MP scores and running time. Divideand-conquer techniques are also a highly competitive alternative to global heuristics such as the parsimony ratchet, especially on the more challenging datasets. 1

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The algorithm selection problem aims at selecting the best algorithm for a given computational problem instance according to some characteristics of the instance. In this dissertation, we first introduce some results from theoretical investigation of the algorithm selection problem. We show, by Rice's theorem, the nonexistence of an automatic algorithm selection program based only on the description of the input instance and the competing algorithms. We also describe an abstract theoretical framework of instance hardness and algorithm performance based on Kolmogorov complexity to show that algorithm selection for search is also incomputable. Driven by the theoretical results, we propose a machine learning-based inductive approach using experimental algorithmic methods and machine learning techniques to solve the algorithm selection problem. Experimentally, we have