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618,010
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
, 2003
"... The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The ..."
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Cited by 2109 (30 self)
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. The core of this method is a simple hillclimbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distancebased method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment
A Fast Algorithm for Particle Simulations
, 1987
"... this paper to the case where the potential (or force) at a point is a sum of pairwise An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles interactions. More specifically, we consider potentials of whose interactions a ..."
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Cited by 1145 (19 self)
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this paper to the case where the potential (or force) at a point is a sum of pairwise An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles interactions. More specifically, we consider potentials of whose interactions
Application of Phylogenetic Networks in Evolutionary Studies
 SUBMITTED TO MBE 2005
, 2005
"... The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evoluti ..."
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Cited by 867 (15 self)
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The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when
Fast Algorithms for Mining Association Rules
, 1994
"... We consider the problem of discovering association rules between items in a large database of sales transactions. We present two new algorithms for solving this problem that are fundamentally different from the known algorithms. Empirical evaluation shows that these algorithms outperform the known a ..."
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Cited by 3551 (15 self)
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We consider the problem of discovering association rules between items in a large database of sales transactions. We present two new algorithms for solving this problem that are fundamentally different from the known algorithms. Empirical evaluation shows that these algorithms outperform the known
A Fast and Elitist MultiObjective Genetic Algorithm: NSGAII
, 2000
"... Multiobjective evolutionary algorithms which use nondominated sorting and sharing have been mainly criticized for their (i) O(MN computational complexity (where M is the number of objectives and N is the population size), (ii) nonelitism approach, and (iii) the need for specifying a sharing param ..."
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Cited by 1707 (58 self)
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parameter. In this paper, we suggest a nondominated sorting based multiobjective evolutionary algorithm (we called it the Nondominated Sorting GAII or NSGAII) which alleviates all the above three difficulties. Specifically, a fast nondominated sorting approach with O(MN ) computational complexity
Comparison of Multiobjective Evolutionary Algorithms: Empirical Results
, 2000
"... In this paper, we provide a systematic comparison of various evolutionary approaches to multiobjective optimization using six carefully chosen test functions. Each test function involves a particular feature that is known to cause difficulty in the evolutionary optimization process, mainly in conver ..."
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Cited by 605 (39 self)
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, the experimental results indicate a hierarchy of the algorithms under consideration. Furthermore, the emerging effects are evidence that the suggested test functions provide sufficient complexity to compare multiobjective optimizers. Finally, elitism is shown to be an important factor for improving evolutionary
FastMap: A Fast Algorithm for Indexing, DataMining and Visualization of Traditional and Multimedia Datasets
, 1995
"... A very promising idea for fast searching in traditional and multimedia databases is to map objects into points in kd space, using k featureextraction functions, provided by a domain expert [25]. Thus, we can subsequently use highly finetuned spatial access methods (SAMs), to answer several types ..."
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Cited by 497 (23 self)
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domain expert to assess the similarity/distance of two objects. Given only the distance information though, it is not obvious how to map objects into points. This is exactly the topic of this paper. We describe a fast algorithm to map objects into points in some kdimensional space (k is user
Fast Parallel Algorithms for ShortRange Molecular Dynamics
 JOURNAL OF COMPUTATIONAL PHYSICS
, 1995
"... Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dyn ..."
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Cited by 622 (6 self)
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Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of interatomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular
MEGA5: Molecular evolutionary genetics analysis using maximum . . .
, 2011
"... Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version ..."
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Cited by 6858 (19 self)
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) analyses for inferring evolutionary trees, selecting bestfit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates sitebysite. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared
Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package)
"... Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and bas ..."
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Cited by 812 (119 self)
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Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions
Results 1  10
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618,010