Bioinformatics Vol. 19 no. 12 2003
Pages 1572-1574
© 2003 Oxford University Press
Applications Note |
MrBayes 3: Bayesian phylogenetic inference under mixed models
1 Department of Systematic Zoology, Evolutionary Biology
Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden
2 Section of Ecology, Behavior and Evolution, Division
of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0116,
USA
Received on December 20, 2002
; revised on February 14, 2003
; accepted on February 19, 2003
Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters.
Availability: http://morphbank.ebc.uu.se/mrbayes
Contact: fredrik.ronquist{at}ebc.uu.se
* To whom correspondence should be addressed.
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M. M. Van der Merwe, M. W. Kinnear, L. G. Barrett, P. N. Dodds, L. Ericson, P. H. Thrall, and J. J. Burdon Positive selection in AvrP4 avirulence gene homologues across the genus Melampsora Proc R Soc B, August 22, 2009; 276(1669): 2913 - 2922. [Abstract] [Full Text] [PDF]
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A. T. Beckenbach and J. B. Joy Evolution of the Mitochondrial Genomes of Gall Midges (Diptera: Cecidomyiidae): Rearrangement and Severe Truncation of tRNA Genes Gen Biol Evol, August 21, 2009; 2009(0): 278 - 287. [Abstract] [Full Text] [PDF]
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D. San Mauro, D. J. Gower, T. Massingham, M. Wilkinson, R. Zardoya, and J. A. Cotton Experimental Design in Caecilian Systematics: Phylogenetic Information of Mitochondrial Genomes and Nuclear rag1 Syst Biol, August 18, 2009; (2009) syp043v1. [Abstract] [Full Text] [PDF]
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G. R. Burke, B. B. Normark, C. Favret, and N. A. Moran Evolution and Diversity of Facultative Symbionts from the Aphid Subfamily Lachninae Appl. Envir. Microbiol., August 15, 2009; 75(16): 5328 - 5335. [Abstract] [Full Text] [PDF]
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P.-A. Christin, E. Samaritani, B. Petitpierre, N. Salamin, and G. Besnard Evolutionary Insights on C4 Photosynthetic Subtypes in Grasses from Genomics and Phylogenetics Gen Biol Evol, August 13, 2009; 2009(0): 221 - 230. [Abstract] [Full Text] [PDF]
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 P. G. Foster, C. J. Cox, and T. M. Embley The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods Phil Trans R Soc B, August 12, 2009; 364(1527): 2197 - 2207. [Abstract] [Full Text] [PDF]
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 L. A. Nahum, S. Goswami, and M. H. Serres Protein families reflect the metabolic diversity of organisms and provide support for functional prediction Physiol Genomics, August 7, 2009; 38(3): 250 - 260. [Abstract] [Full Text] [PDF]
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H. Liu, I. Probert, J. Uitz, H. Claustre, S. Aris-Brosou, M. Frada, F. Not, and C. de Vargas Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans PNAS, August 4, 2009; 106(31): 12803 - 12808. [Abstract] [Full Text] [PDF]
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G. C. Amico and D. L. Nickrent Population structure and phylogeography of the mistletoes Tristerix corymbosus and T. aphyllus (Loranthaceae) using chloroplast DNA sequence variation Am. J. Botany, August 1, 2009; 96(8): 1571 - 1580. [Abstract] [Full Text] [PDF]
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W. F. Fricke, T. J. Welch, P. F. McDermott, M. K. Mammel, J. E. LeClerc, D. G. White, T. A. Cebula, and J. Ravel Comparative Genomics of the IncA/C Multidrug Resistance Plasmid Family J. Bacteriol., August 1, 2009; 191(15): 4750 - 4757. [Abstract] [Full Text] [PDF]
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M. T. Cottrell and D. L. Kirchman Photoheterotrophic Microbes in the Arctic Ocean in Summer and Winter Appl. Envir. Microbiol., August 1, 2009; 75(15): 4958 - 4966. [Abstract] [Full Text] [PDF]
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M. C. De Aranzamendi, C. N. Gardenal, J. P. Martin, and R. Bastida Limpets of the genus Nacella (Patellogastropoda) from the Southwestern Atlantic: species identification based on molecular data J. Mollus. Stud., August 1, 2009; 75(3): 241 - 251. [Abstract] [Full Text] [PDF]
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L. Liu and S. V. Edwards Phylogenetic Analysis in the Anomaly Zone Syst Biol, August 1, 2009; 58(4): 452 - 460. [Full Text] [PDF]
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N. C. Sheffield, H. Song, S. L. Cameron, and M. F. Whiting Nonstationary Evolution and Compositional Heterogeneity in Beetle Mitochondrial Phylogenomics Syst Biol, August 1, 2009; 58(4): 381 - 394. [Abstract] [Full Text] [PDF]
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B. Nitz, R. Heim, U. E. Schneppat, I. Hyman, and G. Haszprunar Towards a new standard in slug species descriptions: the case of Limax sarnensis Heim & Nitz n. sp. (Pulmonata: Limacidae) from the Western Central Alps J. Mollus. Stud., August 1, 2009; 75(3): 279 - 294. [Abstract] [Full Text] [PDF]
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 C. van den Berg, W. E. Higgins, R. L. Dressler, W. M. Whitten, M. A. Soto-Arenas, and M. W. Chase A phylogenetic study of Laeliinae (Orchidaceae) based on combined nuclear and plastid DNA sequences Ann. Bot., August 1, 2009; 104(3): 417 - 430. [Abstract] [Full Text] [PDF]
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