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The Phylogenetic Likelihood Library

We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, er... Full description

Journal Title: Systematic Biology 2015-03-01, Vol.64 (2), p.356-362
Main Author: Flouri, T
Other Authors: Izquierdo-Carrasco, F , Darriba, D , Aberer, A.J , Nguyen, L.-T , Minh, B.Q , Von Haeseler, A , Stamatakis, A
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: England: Oxford University Press
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/25358969
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recordid: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4380035
title: The Phylogenetic Likelihood Library
format: Article
creator:
  • Flouri, T
  • Izquierdo-Carrasco, F
  • Darriba, D
  • Aberer, A.J
  • Nguyen, L.-T
  • Minh, B.Q
  • Von Haeseler, A
  • Stamatakis, A
subjects:
  • Algorithms
  • Application programming interface
  • Classification - methods
  • Evolution
  • Libraries, Digital
  • Maximum likelihood
  • Optimization
  • parallel computing
  • Phylogenetics
  • Phylogeny
  • Software
  • Software - standards
  • Software for Systematics
  • SOFTWARE FOR SYSTEMATICS AND EVOLUTION
  • Systematic biology
ispartof: Systematic Biology, 2015-03-01, Vol.64 (2), p.356-362
description: We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www. libpll. org under the GNU General Public License (GPL).
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


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descriptionWe introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www. libpll. org under the GNU General Public License (GPL).
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subjectAlgorithms ; Application programming interface ; Classification - methods ; Evolution ; Libraries, Digital ; Maximum likelihood ; Optimization ; parallel computing ; Phylogenetics ; Phylogeny ; Software ; Software - standards ; Software for Systematics ; SOFTWARE FOR SYSTEMATICS AND EVOLUTION ; Systematic biology
ispartofSystematic Biology, 2015-03-01, Vol.64 (2), p.356-362
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0Copyright © 2015 Society of Systematic Biologists
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descriptionWe introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www. libpll. org under the GNU General Public License (GPL).
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abstractWe introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implementation of the phylogenetic likelihood function and a thorough documentation provide a framework for rapid development of scalable parallel phylogenetic software. By example of two likelihood-based phylogenetic codes we show that the PLL improves the sequential performance of current software by a factor of 2-10 while requiring only 1 month of programming time for integration. We show that, when numerical scaling for preventing floating point underflow is enabled, the double precision likelihood calculations in the PLL are up to 1.9 times faster than those in BEAGLE. On an empirical DNA dataset with 2000 taxa the AVX version of PLL is 4 times faster than BEAGLE (scaling enabled and required). The PLL is available at http://www. libpll. org under the GNU General Public License (GPL).
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