论文信息 - Bayesian Phylogenetic Inference in the LIBI Grid Platform: A Tool to Explore Large Data Sets

Bayesian Phylogenetic Inference in the LIBI Grid Platform: A Tool to Explore Large Data Sets

This works presents the porting on the grid of a parallel application of phylogenetic inference, MrBayes, in the LIBI (International Laboratory of Bioinformatics) platform. Moreover a bioinformatic case study about the analysis of 11 phylogenies, including a series of large sequences data sets that represent the nascent barcode reference database for Lepidoptera is also presented. The case study has been tested on the platform and the speedup and efficiency on Itanium HP XC6000 (Intel Itanium 2 processors and Quadrics interconnects) of the SPACI consortium, University of Salento, are described.

[1] G. Serio,et al. A new method for calculating evolutionary substitution rates , 2005, Journal of Molecular Evolution.

[2] Sandhya Dwarkadas,et al. Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference , 2002, Bioinform..

[3] Jonathan P. Bollback,et al. Bayesian model adequacy and choice in phylogenetics. , 2002, Molecular biology and evolution.

[4] Sylvia Richardson,et al. Markov Chain Monte Carlo in Practice , 1997 .

[5] C. Geyer. Markov Chain Monte Carlo Maximum Likelihood , 1991 .

[6] Ziheng Yang. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.

[7] Izabela Makalowska,et al. FUSARIUM-ID v. 1.0: A DNA Sequence Database for Identifying Fusarium , 2004, European Journal of Plant Pathology.

[8] Ernesto Picardi,et al. The LIBI Grid Platform an International Laboratory for Bioinformatics , 2008 .

[9] P. Hebert,et al. bold: The Barcode of Life Data System (http://www.barcodinglife.org) , 2007, Molecular ecology notes.

[10] P. Hebert,et al. bold: The Barcode of Life Data System (http://www.barcodinglife.org) , 2007, Molecular ecology notes.

[11] David L. Erickson,et al. DNA barcodes: Genes, genomics, and bioinformatics , 2008, Proceedings of the National Academy of Sciences.

[12] John P. Huelsenbeck,et al. MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..