Accelerating the phylogenetic parsimony function on heterogeneous systems: Accelerating the phylogenetic parsimony function on heterogeneous systems
- Authors:
-
- Department of Computer and Communications Technologies, University of Extremadura, Escuela Politécnica, Campus Universitario s/n, Cáceres 10003 Spain
- INESC-ID, IST, Universidade de Lisboa, Lisboa 1000-029 Portugal
- Publication Date:
- Sponsoring Org.:
- USDOE Office of Nuclear Energy (NE), Fuel Cycle Technologies (NE-5)
- OSTI Identifier:
- 1401259
- Grant/Contract Number:
- UID/CEC/50021/2013; PTDC/EEI-ELC/3152/2012; FPU12/04101; ACCION-III-04
- Resource Type:
- Publisher's Accepted Manuscript
- Journal Name:
- Concurrency and Computation. Practice and Experience
- Additional Journal Information:
- Journal Name: Concurrency and Computation. Practice and Experience Journal Volume: 29 Journal Issue: 8; Journal ID: ISSN 1532-0626
- Publisher:
- Wiley Blackwell (John Wiley & Sons)
- Country of Publication:
- United Kingdom
- Language:
- English
Citation Formats
Santander-Jiménez, Sergio, Ilic, Aleksandar, Sousa, Leonel, and Vega-Rodríguez, Miguel A. Accelerating the phylogenetic parsimony function on heterogeneous systems: Accelerating the phylogenetic parsimony function on heterogeneous systems. United Kingdom: N. p., 2016.
Web. doi:10.1002/cpe.4046.
Santander-Jiménez, Sergio, Ilic, Aleksandar, Sousa, Leonel, & Vega-Rodríguez, Miguel A. Accelerating the phylogenetic parsimony function on heterogeneous systems: Accelerating the phylogenetic parsimony function on heterogeneous systems. United Kingdom. https://doi.org/10.1002/cpe.4046
Santander-Jiménez, Sergio, Ilic, Aleksandar, Sousa, Leonel, and Vega-Rodríguez, Miguel A. Fri .
"Accelerating the phylogenetic parsimony function on heterogeneous systems: Accelerating the phylogenetic parsimony function on heterogeneous systems". United Kingdom. https://doi.org/10.1002/cpe.4046.
@article{osti_1401259,
title = {Accelerating the phylogenetic parsimony function on heterogeneous systems: Accelerating the phylogenetic parsimony function on heterogeneous systems},
author = {Santander-Jiménez, Sergio and Ilic, Aleksandar and Sousa, Leonel and Vega-Rodríguez, Miguel A.},
abstractNote = {},
doi = {10.1002/cpe.4046},
journal = {Concurrency and Computation. Practice and Experience},
number = 8,
volume = 29,
place = {United Kingdom},
year = {Fri Dec 23 00:00:00 EST 2016},
month = {Fri Dec 23 00:00:00 EST 2016}
}
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https://doi.org/10.1002/cpe.4046
https://doi.org/10.1002/cpe.4046
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Cited by: 1 work
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Works referenced in this record:
Life-history evolution and mitogenomic phylogeny of caecilian amphibians
journal, April 2014
- San Mauro, Diego; Gower, David J.; Müller, Hendrik
- Molecular Phylogenetics and Evolution, Vol. 73
Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology
journal, December 1971
- Fitch, Walter M.
- Systematic Zoology, Vol. 20, Issue 4
Resource-efficient utilization of CPU/GPU-based heterogeneous supercomputers for Bayesian phylogenetic inference
journal, March 2013
- Chai, Jun; Su, Huayou; Wen, Mei
- The Journal of Supercomputing, Vol. 66, Issue 1
Large-scale analysis of NBS domain-encoding resistance gene analogs in Triticeae
journal, September 2014
- Bouktila, Dhia; Khalfallah, Yosra; Habachi-Houimli, Yosra
- Genetics and Molecular Biology, Vol. 37, Issue 3
Parallel implementation of DNAml program on message-passing architectures
journal, June 1998
- Ceron, C.; Dopazo, J.; Zapata, E. L.
- Parallel Computing, Vol. 24, Issue 5-6
Genetic Algorithms and Parallel Processing in Maximum-Likelihood Phylogeny Inference
journal, October 2002
- Brauer, Matthew J.; Holder, Mark T.; Dries, Laurie A.
- Molecular Biology and Evolution, Vol. 19, Issue 10
High-Performance Algorithm Engineering for Computational Phylogenetics
journal, January 2002
- Moret, Bernard M. E.; Bader, David A.; Warnow, Tandy
- The Journal of Supercomputing, Vol. 22, Issue 1, p. 99-111
BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
journal, October 2011
- Ayres, Daniel L.; Darling, Aaron; Zwickl, Derrick J.
- Systematic Biology, Vol. 61, Issue 1
Fast Fitch-Parsimony Algorithms for Large Data Sets
journal, December 1998
- Ronquist, Fredrik
- Cladistics, Vol. 14, Issue 4
Comparing Hardware Accelerators in Scientific Applications: A Case Study
journal, January 2011
- Weber, Rick; Gothandaraman, Akila; Hinde, Robert J.
- IEEE Transactions on Parallel and Distributed Systems, Vol. 22, Issue 1
A Survey of Parallel Programming Models and Tools in the Multi and Many-Core Era
journal, August 2012
- Diaz, Javier; Munoz-Caro, Camelia; Nino, Alfonso
- IEEE Transactions on Parallel and Distributed Systems, Vol. 23, Issue 8
The Phylogenetic Handbook
book, March 2009
- Lemey, Philippe; Salemi, Marco; Vandamme, Anne-Mieke
- Cambridge University Press
Many-core algorithms for statistical phylogenetics
journal, April 2009
- Suchard, M. A.; Rambaut, A.
- Bioinformatics, Vol. 25, Issue 11
Phylogenetic Diversity of the Enteric Pathogen Salmonella enterica subsp. enterica Inferred from Genome-Wide Reference-Free SNP Characters
journal, October 2013
- Timme, Ruth E.; Pettengill, James B.; Allard, Marc W.
- Genome Biology and Evolution, Vol. 5, Issue 11
The Phylogenetic Likelihood Library
journal, October 2014
- Flouri, T.; Izquierdo-Carrasco, F.; Darriba, D.
- Systematic Biology, Vol. 64, Issue 2
Efficient Implementation of MrBayes on Multi-GPU
journal, March 2013
- Bao, J.; Xia, H.; Zhou, J.
- Molecular Biology and Evolution, Vol. 30, Issue 6
The computational complexity of inferring rooted phylogenies by parsimony
journal, September 1986
- Day, William H. E.; Johnson, David S.; Sankoff, David
- Mathematical Biosciences, Vol. 81, Issue 1
Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures
journal, October 2008
- Stamatakis, Alexandros; Ott, Michael
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 363, Issue 1512
How should gaps be treated in parsimony? A comparison of approaches using simulation
journal, March 2007
- Ogden, T. Heath; Rosenberg, Michael S.
- Molecular Phylogenetics and Evolution, Vol. 42, Issue 3
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
journal, February 2012
- Ronquist, Fredrik; Teslenko, Maxim; van der Mark, Paul
- Systematic Biology, Vol. 61, Issue 3
Parallel Multiobjective Metaheuristics for Inferring Phylogenies on Multicore Clusters
journal, June 2015
- Santander-Jimenez, Sergio; Vega-Rodriguez, Miguel A.
- IEEE Transactions on Parallel and Distributed Systems, Vol. 26, Issue 6
Next-generation DNA sequencing
journal, October 2008
- Shendure, Jay; Ji, Hanlee
- Nature Biotechnology, Vol. 26, Issue 10
Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles
journal, January 2010
- Thomson, Robert C.; Shaffer, H. Bradley
- Systematic Biology, Vol. 59, Issue 1
Fine-grain parallelism using multi-core, Cell/BE, and GPU Systems
journal, August 2012
- Pratas, Frederico; Trancoso, Pedro; Sousa, Leonel
- Parallel Computing, Vol. 38, Issue 8
Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
journal, September 2011
- Meredith, R. W.; Janecka, J. E.; Gatesy, J.
- Science, Vol. 334, Issue 6055
Dynamic Load Balancing on Dedicated Heterogeneous Systems
book, January 2008
- Galindo, Ismael; Almeida, Francisco; Badía-Contelles, José Manuel
- Recent Advances in Parallel Virtual Machine and Message Passing Interface
Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL
journal, January 1993
- Chase, Mark W.; Soltis, Douglas E.; Olmstead, Richard G.
- Annals of the Missouri Botanical Garden, Vol. 80, Issue 3
Bio++: Efficient Extensible Libraries and Tools for Computational Molecular Evolution
journal, May 2013
- Guéguen, Laurent; Gaillard, Sylvain; Boussau, Bastien
- Molecular Biology and Evolution, Vol. 30, Issue 8