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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...

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The combination of a Markov chain Monte Carlo (MCMC) method with likelihood-based assessment of phylogenies is becoming a popular alternative to direct likelihood optimization. However, MCMC, like maximum likelihood, is a computationallyexpensive method. To approximate the posterior distribution of phylogenies, a Markov chain is constructed, using the Metropolis algorithm, such that the chain has the posterior distribution of the parameters of phylogenies as its stationary distribution. This paper describes parallel algorithms and their MPI-based parallel implementation for MCMC-based Bayesian phylogenetic inference. Bayesian phylogenetic inference is computationally expensive both in time and in memory requirements. Our variations on MCMC and their implementation were done to permit the studyof large phylogenetic problems. In our approach, we can distribute either entire chains or parts of a chain to different processors, since in current models the columns of the data are independent. Evaluations on a 32-node Beowulf cluster suggest the problem scales well. A number of important points are identified, including a superlinear speedup due to more effective cache usage and the point at which additional processors slow down the process due to communication overhead.

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This paper describes the implementation and performance of PBPI, a parallel implementation of Bayesian phylogenetic inference method for DNA sequence data. By combining the Markov Chain Monte Carlo (MCMC) method with likelihood-based assessment of phylogenies, Bayesian phylogenetic inferences can incorporate complex statistic models into the process of phylogenetic tree estimation. However, Bayesian analyses are extremely computationally expensive. PBPI uses algorithmic improvements and parallel processing to achieve significant performance improvement over comparable Bayesian phylogenetic inference programs. We evaluated the performance and accuracy of PBPI using a simulated dataset on System X, a terascale supercomputer at Virginia Tech. Our results show that PBPI identifies equivalent tree estimates 1424 times faster on 256 processors than a widely-used, best-available (albeit sequential), Bayesian phylogenetic inference program. PBPI also achieves linear speedup with the number of processors for large problem sizes. Most importantly, the PBPI framework enables Bayesian phylogenetic analysis of large datasets previously impracticable. 1.

Abstract. The computation of ever larger as well as more accurate phylogenetic (evolutionary) trees with the ultimate goal to compute the tree of life represents one of the grand challenges in High Performance Computing (HPC) Bioinformatics. Unfortunately, the size of trees which can be computed in reasonable time based on elaborate evolutionary models is limited by the severe computational cost inherent to these methods. There exist two orthogonal research directions to overcome this challenging computational burden: First, the development of novel, faster, and more accurate heuristic algorithms and second, the application of high performance computing techniques. The goal of this chapter is to provide a comprehensive introduction to the field of computational evolutionary biology to an audience with computing background, interested in participating in research and/or commercial applications of this field. Moreover, we will cover leading-edge technical and algorithmic developments in the field and discuss open problems and potential solutions.

With breakpoint distance, the genome rearrangement field delivered one of the currently most popular measures in phylogenetic studies for related species. Here, BREAK- POINT MEDIAN, which is NP-complete already for three given species (whose genomes are represented as signed orderings), is the core basic problem. For the important special case of three species, approximation (ratio 7/6) and exact heuristic algorithms were developed. Here, we provide an exact, fixed-parameter algorithm with provable performance bounds. For instance, a breakpoint median for three signed orderings over n elements that causes at most d breakpoints can be computed in time O((2.15) n). We show the algorithm's practical usefulness through experimental studies. In particular, we demonstrate that a simple implementation of our algorithm combined with a new tree construction heuristic allows for a new approach to breakpoint phylogeny, yielding evolutionary trees that are competitive in comparison with known results developed in a recent series of papers that use clever algorithm engineering methods.