Industrial applications of high-performance computing for phylogeny reconstruction

No abstract is available for this paper.

• Publication year

  2001

• Venue

  SPIE ITCom

• Publication date

  2001-07-27

• Fields of study

  Computer Science, Engineering

• Identifiers
  DOI 10.1117/12.434868
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• 8. The traveling salesman problem: a case study

  2003cited by this paper
• A detailed study of breakpoint analysis

  2001cited by this paper
• Cloning, expression, and pharmacological characterization of a novel human histamine receptor.

  2001cited by this paper
• A fast linear-time algorithm for inversion distance with an experimental comparison

  2001cited by this paper
• A New Implmentation and Detailed Study of Breakpoint Analysis

  2000cited by this paper
• WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction

  2000cited by this paper
• Improving memory performance of sorting algorithms

  2000cited by this paper
• Efficient sorting using registers and caches

  2000cited by this paper
• An Empirical Comparison of Phylogenetic Methods on Chloroplast Gene Order Data in Campanulaceae

  2000cited by this paper
• Neuromedin U Is a Potent Agonist at the Orphan G Protein-coupled Receptor FM3*

  2000cited by this paper
• Identification, Evolution, and Essentiality of the Mevalonate Pathway for Isopentenyl Diphosphate Biosynthesis in Gram-Positive Cocci

  2000cited by this paper
• A G Protein-coupled Receptor for UDP-glucose*

  2000cited by this paper
• GRAPPA runs in record time

  2000cited by this paper
• A new fast heuristic for computing the breakpoint phylogeny and a phylogenetic analysis of a group of highly rearranged chloroplast genomes

  2000cited by this paper
• Cache-oblivious algorithms

  1999cited by this paper
• Cache performance analysis of traversals and random accesses

  1999cited by this paper
• Matrix multiplication: a case study of enhanced data cache utilization

  1999cited by this paper
• The median problems for breakpoints are NP-complete

  1998cited by this paper
• Evidence for the shikimate pathway in apicomplexan parasites

  1998cited by this paper
• Multiple Genome Rearrangement and Breakpoint Phylogeny

  1998cited by this paper
• Antibiotic discovery: is it all in the genes?

  1998cited by this paper
• Monitoring Impact of a Pesticide Treatment on Bacterial Soil Communities by Metabolic and Genetic Fingerprinting in Addition to Conventional Testing Procedures

  1998cited by this paper
• Breakpoint Phylogenies.

  1997cited by this paper
• The influence of caches on the performance of heaps

  1996cited by this paper
• Chloroplast DNA systematics: a review of methods and data analysis

  1994cited by this paper
• Chloroplast DNA Evidence on the Ancient Evolutionary Split in Vascular Land Plants

  1992cited by this paper
• The herbicide glyphosate.

  1989cited by this paper
• The neighbor-joining method: a new method for reconstructing phylogenetic trees.

  1987cited by this paper
• The neighbor-joining method

  1987cited by this paper
• DIMACS Series in Discrete Mathematics and Theoretical Computer Science Towards a Discipline of Experimental Algorithmics

  year unknowncited by this paper

• Scalable Phylogeny Reconstruction with Disaggregated Near-memory Processing

  2021cites this paper
• A tutorial on the balanced minimum evolution problem

  2021cites this paper
• Load-Balance and Fault-Tolerance for Massively Parallel Phylogenetic Inference

  2020cites this paper
• Molecular systematics of rattans of South India

  2019cites this paper
• Phylogenetic Analysis of Freshwater Mussel (Bivalvia: Unionoida)

  2018cites this paper
• RAxML-CELL: Parallel Phylogenetic Tree Construction on the Cell Broadband Engine

  2018cites this paper
• Engineering Algorithms for Large Network Applications

  2016cites this paper
• Hadoop-Based Algorithm for Inference of Phylogenetic Trees Using Maximum Likelihood Method

  2016cites this paper
• The Minimum Evolution Criterion of Phylogeny Estimation via Linear Programming: Theoretical Foundations and Improved Solution Approaches

  2015cites this paper
• A branch-price-and-cut algorithm for the minimum evolution problem

  2015cites this paper
• The balanced minimum evolution problem under uncertain data

  2013cites this paper
• A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion

  2013cites this paper
• Resource-efficient utilization of CPU/GPU-based heterogeneous supercomputers for Bayesian phylogenetic inference

  2013cites this paper
• Algorithms and Computer Architectures for Evolutionary Bioinformatics

  2012cites this paper
• Computational Challenges in Emerging Combinatorial Scientific Computing Applications

  2012cites this paper
• The Balanced Minimum Evolution Problem

  2012cites this paper
• Algorithms for Model Assignment in MultiGene Phylogenetics

  2012cites this paper
• Estimating Phylogenies from Molecular Data

  2010cites this paper
• Large-scale analysis of phylogenetic search behavior.

  2010cites this paper
• Preparing RAxML for the SPEC MPI Benchmark Suite

  2010cites this paper
• The minimum evolution problem: Overview and classification

  2009cites this paper
• ParBaum: Large-Scale Maximum Likelihood-Based Phylogenetic Analyses

  2009cites this paper
• Using tree diversity to compare phylogenetic heuristics

  2009cites this paper
• Exploring FPGAs for accelerating the phylogenetic likelihood function

  2009cites this paper
• A note on trees, tables, and algorithms

  2009cites this paper
• Large-scale phylogenetic analysis on current HPC architectures

  2008cites this paper
• Estimating phylogenies under maximum likelihood : A very large-scale neighborhood approach

  2008cites this paper
• BIOINVIEW: A SYSTEM FOR INTEGRATING HETEROGENEOUS AND DISTRIBUTED BIOLOGICAL DATA SOURCES

  2008cites this paper
• Scheduling on Asymmetric Parallel Architectures

  2008cites this paper
• New Approaches to Compare Phylogenetic Search Heuristics

  2008cites this paper
• Engineering Algorithms for Computational Biology

  2008cites this paper
• A study on efficiency of recursive algorithm for estimating relationship coefficients

  2007cites this paper
• Dynamic multigrain parallelization on the cell broadband engine

  2007cites this paper
• Runtime scheduling of dynamic parallelism on accelerator-based multi-core systems

  2007cites this paper
• Exploring New Search Algorithms and Hardware for Phylogenetics: RAxML Meets the IBM Cell

  2007cites this paper
• Large-scale maximum likelihood-based phylogenetic analysis on the IBM BlueGene/L

  2007cites this paper
• Parallelization of the maximum likelihood approach to phylogenetic inference

  2007cites this paper
• Phylogenetics in plant biotechnology: principles, obstacles and opportunities for the resource poor

  2007cites this paper
• RAxML-Cell: Parallel Phylogenetic Tree Inference on the Cell Broadband Engine

  2007cites this paper
• High‐Performance Phylogeny Reconstruction Under Maximum Parsimony

  2006cites this paper
• High-performance Computing Methods for Computational Genomics

  2006cites this paper
• Phylogenetic models of rate heterogeneity: a high performance computing perspective

  2006cites this paper
• Exploring Programming Models and Optimizations for the Cell Broadband Engine using RAxML

  2006cites this paper
• Computational Grand Challenges in Assembling the Tree of Life: Problems and Solutions

  2006cites this paper
• Computational Challenges from the Tree of Life

  2005cites this paper
• Phylogenetics: Applications, Software and Challenges.

  2005cites this paper
• A GRASP/VND heuristic for the phylogeny problem using a new neighborhood structure

  2005cites this paper
• RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs

  2005cites this paper
• Cooperative Rec-I-DCM3: A Population-Based Approach for Reconstructing Phylogenies

  2005cites this paper
• Parallel Algorithm Design for Branch and Bound

  2005cites this paper
• Using Treemaps to Visualize Phylogenetic Trees

  2005cites this paper
• An efficient program for phylogenetic inference using simulated annealing

  2005cites this paper
• Initial Experiences Porting a Bioinformatics Application to a Graphics Processor

  2005cites this paper
• High-Performance Algorithm Engineering for Large-Scale Graph Problems and Computational Biology

  2005cites this paper
• Network (Reticulated) Evolution: Biology, Models, and Algorithms

  2004cites this paper
• Network ( Reticulate ) Evolution : Biology , Models , and Algorithms

  2004cites this paper
• Chapter 5 PARALLEL ALGORITHM DESIGN FOR BRANCH AND BOUND

  2004cites this paper
• 1 High-Performance Phylogeny Reconstruction Under Maximum Parsimony

  2004cites this paper
• Implementation of Load Balancing Policies in Distributed Systems

  2004cites this paper
• An investigation of phylogenetic likelihood methods

  2003cites this paper
• High-Performance Algorithm Engineering for Computational Phylogenetics

  2001cites this paper
• European Journal of Operational Research a Branch-price-and-cut Algorithm for the Minimum Evolution Problem

  year unknowncites this paper
• Integrating Campaign Storage into HPC Workflows

  year unknowncites this paper