ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

被引：365

作者：

Aberer, Andre J. ^{[1
]}

Kobert, Kassian ^{[1
]}

Stamatakis, Alexandros ^{[1
,2
]}

机构：

[1] Heidelberg Inst Theoret Studies, Sci Comp Grp, Heidelberg, Germany

[2] Karlsruhe Inst Technol, Inst Theoret Informat, D-76021 Karlsruhe, Germany

来源：

MOLECULAR BIOLOGY AND EVOLUTION | 2014年 / 31卷 / 10期

关键词：

software; Bayesian statistics; phylogenetic inference; whole-genome analyses; parallelization; CHAIN MONTE-CARLO; PHYLOGENETIC INFERENCE; ALGORITHMS;

D O I：

10.1093/molbev/msu236

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Modern sequencing technology now allows biologists to collect the entirety of molecular evidence for reconstructing evolutionary trees. We introduce a novel, user-friendly software package engineered for conducting state-of-the-art Bayesian tree inferences on data sets of arbitrary size. Our software introduces a nonblocking parallelization of Metropolis-coupled chains, modifications for efficient analyses of data sets comprising thousands of partitions and memory saving techniques. We report on first experiences with Bayesian inferences at the whole-genome level using the SuperMUC supercomputer and simulated data.

引用

页码：2553 / 2556

页数：4

共 18 条

[1] Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference [J].

Altekar, G ;

Dwarkadas, S ;

Huelsenbeck, JP ;

Ronquist, F .

BIOINFORMATICS, 2004, 20 (03) :407-415

[2] Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects [J].

Dell'Ampio, Emiliano ;

Meusemann, Karen ;

Szucsich, Nikolaus U. ;

Peters, Ralph S. ;

Meyer, Benjamin ;

Borner, Janus ;

Petersen, Malte ;

Aberer, Andre J. ;

Stamatakis, Alexandros ;

Walzl, Manfred G. ;

Minh, Bui Quang ;

von Haeseler, Arndt ;

Ebersberger, Ingo ;

Pass, Guenther ;

Misof, Bernhard .

MOLECULAR BIOLOGY AND EVOLUTION, 2014, 31 (01) :239-249

[3]

Drummond A.J., 2014, FigTree 1.4. 2 software

[4] Bayesian Phylogenetics with BEAUti and the BEAST 1.7 [J].

Drummond, Alexei J. ;

Suchard, Marc A. ;

Xie, Dong ;

Rambaut, Andrew .

MOLECULAR BIOLOGY AND EVOLUTION, 2012, 29 (08) :1969-1973

[5] Broad phylogenomic sampling improves resolution of the animal tree of life [J].

Dunn, Casey W. ;

Hejnol, Andreas ;

Matus, David Q. ;

Pang, Kevin ;

Browne, William E. ;

Smith, Stephen A. ;

Seaver, Elaine ;

Rouse, Greg W. ;

Obst, Matthias ;

Edgecombe, Gregory D. ;

Sorensen, Martin V. ;

Haddock, Steven H. D. ;

Schmidt-Rhaesa, Andreas ;

Okusu, Akiko ;

Kristensen, Reinhardt Mobjerg ;

Wheeler, Ward C. ;

Martindale, Mark Q. ;

Giribet, Gonzalo .

NATURE, 2008, 452 (7188) :745-U5

[6] CONSTRUCTION OF PHYLOGENETIC TREES [J].

FITCH, WM ;

MARGOLIASH, E .

SCIENCE, 1967, 155 (3760) :279-+

[7]

Geyer C.J, 1991, COMPUTING SCI STAT 2, P156

[8] New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 [J].

Guindon, Stephane ;

Dufayard, Jean-Francois ;

Lefort, Vincent ;

Anisimova, Maria ;

Hordijk, Wim ;

Gascuel, Olivier .

SYSTEMATIC BIOLOGY, 2010, 59 (03) :307-321

[9] MONTE-CARLO SAMPLING METHODS USING MARKOV CHAINS AND THEIR APPLICATIONS [J].

HASTINGS, WK .

BIOMETRIKA, 1970, 57 (01) :97-&

[10] Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees [J].

Izquierdo-Carrasco, Fernando ;

Smith, Stephen A. ;

Stamatakis, Alexandros .

BMC BIOINFORMATICS, 2011, 12

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