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.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  N. Iritani, H. Vennema, J. J. Siebenga, R. J. Siezen, B. Renckens, Y. Seto, A. Kaida, and M. Koopmans Genetic Analysis of the Capsid Gene of Genotype GII.2 Noroviruses J. Virol., August 1, 2008; 82(15): 7336 - 7345. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Ueda, T. Nishikawa, M. Fujimoto, H. Takanashi, S.-i. Arimura, N. Tsutsumi, and K.-i. Kadowaki Substitution of the Gene for Chloroplast RPS16 Was Assisted by Generation of a Dual Targeting Signal Mol. Biol. Evol., August 1, 2008; 25(8): 1566 - 1575. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. J. Krug, M. S. Morley, J. Asif, L. L. Hellyar, and W. M. Blom MOLECULAR CONFIRMATION OF SPECIES STATUS FOR THE RARE CEPHALASPIDEAN MELANOCHLAMYS LORRAINAE (RUDMAN, 1968), AND COMPARISON WITH ITS SISTER SPECIES M. CYLINDRICA CHEESEMAN, 1881 J. Mollus. Stud., July 17, 2008; (2008) eyn018v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Tooming-Klunderud, B. Mikalsen, T. Kristensen, and K. S. Jakobsen The mosaic structure of the mcyABC operon in Microcystis Microbiology, July 1, 2008; 154(7): 1886 - 1899. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. H. Slamovits and P. J. Keeling Plastid-Derived Genes in the Nonphotosynthetic Alveolate Oxyrrhis marina Mol. Biol. Evol., July 1, 2008; 25(7): 1297 - 1306. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Gruenheit, P. J. Lockhart, M. Steel, and W. Martin Difficulties in Testing for Covarion-Like Properties of Sequences under the Confounding Influence of Changing Proportions of Variable Sites Mol. Biol. Evol., July 1, 2008; 25(7): 1512 - 1520. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. J. Joyner, R. W. Litaker, and H. W. Paerl Morphological and Genetic Evidence that the Cyanobacterium Lyngbya wollei (Farlow ex Gomont) Speziale and Dyck Encompasses at Least Two Species Appl. Envir. Microbiol., June 15, 2008; 74(12): 3710 - 3717. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Kirkham, S. J. Nixon, M. T. Howes, L. Abi-Rached, D. E. Wakeham, M. Hanzal-Bayer, C. Ferguson, M. M. Hill, M. Fernandez-Rojo, D. A. Brown, et al. Evolutionary analysis and molecular dissection of caveola biogenesis J. Cell Sci., June 15, 2008; 121(12): 2075 - 2086. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Dupas, C. W. Gitau, A. Branca, B. P. Le Ru, and J.-F. Silvain Evolution of a Polydnavirus Gene in Relation to Parasitoid-Host Species Immune Resistance J. Hered., June 13, 2008; (2008) esn047v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Gillor, J. A. C. Vriezen, and M. A. Riley The role of SOS boxes in enteric bacteriocin regulation Microbiology, June 1, 2008; 154(6): 1783 - 1792. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. F. Keele, L. Tazi, S. Gartner, Y. Liu, T. B. Burgon, J. D. Estes, T. C. Thacker, K. A. Crandall, J. C. McArthur, and G. F. Burton Characterization of the Follicular Dendritic Cell Reservoir of Human Immunodeficiency Virus Type 1 J. Virol., June 1, 2008; 82(11): 5548 - 5561. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. E. Lim-Fong, L. A. Regali, and M. G. Haygood Evolutionary Relationships of "Candidatus Endobugula" Bacterial Symbionts and Their Bugula Bryozoan Hosts Appl. Envir. Microbiol., June 1, 2008; 74(11): 3605 - 3609. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. C. Jost, D. M. Hillis, Y. Lu, J. W. Kyle, H. A. Fozzard, and H. H. Zakon Toxin-Resistant Sodium Channels: Parallel Adaptive Evolution across a Complete Gene Family Mol. Biol. Evol., June 1, 2008; 25(6): 1016 - 1024. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Calvignac, J.-M. Terme, S. M. Hensley, P. Jalinot, A. D. Greenwood, and C. Hanni Ancient DNA Identification of Early 20th Century Simian T-Cell Leukemia Virus Type 1 Mol. Biol. Evol., June 1, 2008; 25(6): 1093 - 1098. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Kolaczkowski and J. W. Thornton A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy Mol. Biol. Evol., June 1, 2008; 25(6): 1054 - 1066. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Burri, H. N. Hirzel, N. Salamin, A. Roulin, and L. Fumagalli Evolutionary Patterns of MHC Class II B in Owls and Their Implications for the Understanding of Avian MHC Evolution Mol. Biol. Evol., June 1, 2008; 25(6): 1180 - 1191. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Saito, M. Nishi, M. I. Lim, B. Wu, T. Maeda, H. Hashimoto, T. Takeuchi, D. S. Roos, and T. Asai A Novel GDP-dependent Pyruvate Kinase Isozyme from Toxoplasma gondii Localizes to Both the Apicoplast and the Mitochondrion J. Biol. Chem., May 16, 2008; 283(20): 14041 - 14052. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Yan, H. Liu, T. J. Mohr, J. Jenrette, R. Chiodini, M. Zaccardelli, J. C. Setubal, and B. A. Vinatzer Role of Recombination in the Evolution of the Model Plant Pathogen Pseudomonas syringae pv. tomato DC3000, a Very Atypical Tomato Strain Appl. Envir. Microbiol., May 15, 2008; 74(10): 3171 - 3181. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Kamikawa, Y. Inagaki, and Y. Sako Direct phylogenetic evidence for lateral transfer of elongation factor-like gene PNAS, May 13, 2008; 105(19): 6965 - 6969. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Kuraku, Y. Takio, K. Tamura, H. Aono, A. Meyer, and S. Kuratani Noncanonical role of Hox14 revealed by its expression patterns in lamprey and shark PNAS, May 6, 2008; 105(18): 6679 - 6683. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y Takei, H Hashimoto, K Inoue, T Osaki, K Yoshizawa-Kumagaye, M Tsunemi, T X Watanabe, M Ogoshi, N Minamino, and Y Ueta Central and peripheral cardiovascular actions of adrenomedullin 5, a novel member of the calcitonin gene-related peptide family, in mammals J. Endocrinol., May 1, 2008; 197(2): 391 - 400. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Quan, M. van Vuuren, P. G. Howell, D. Groenewald, and A. J. Guthrie Molecular epidemiology of the African horse sickness virus S10 gene J. Gen. Virol., May 1, 2008; 89(5): 1159 - 1168. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Noppornpanth, Y. Poovorawan, T. X. Lien, S. L. Smits, A. D. M. E. Osterhaus, and B. L. Haagmans Complete genome analysis of hepatitis C virus subtypes 6t and 6u J. Gen. Virol., May 1, 2008; 89(5): 1276 - 1281. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Jorba, R. Campagnoli, L. De, and O. Kew Calibration of Multiple Poliovirus Molecular Clocks Covering an Extended Evolutionary Range J. Virol., May 1, 2008; 82(9): 4429 - 4440. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. A. Crouch, B. M. Glasheen, W. Uddin, B. B. Clarke, and B. I. Hillman Patterns of Diversity in Populations of the Turfgrass Pathogen Colletotrichum cereale as Revealed by Transposon Fingerprint Profiles Crop Sci., May 1, 2008; 48(3): 1203 - 1210. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. G. Saez, A. Zaldivar-Riveron, and L. K. Medlin Molecular systematics of the Pleurochrysidaceae, a family of coastal coccolithophores (Haptophyta) J. Plankton Res., May 1, 2008; 30(5): 559 - 566. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Blancher, M. Bonhomme, B. Crouau-Roy, K. Terao, T. Kitano, and N. Saitou Mitochondrial DNA Sequence Phylogeny of 4 Populations of the Widely Distributed Cynomolgus Macaque (Macaca fascicularis fascicularis) J. Hered., May 1, 2008; 99(3): 254 - 264. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kurabayashi, M. Sumida, H. Yonekawa, F. Glaw, M. Vences, and M. Hasegawa Phylogeny, Recombination, and Mechanisms of Stepwise Mitochondrial Genome Reorganization in Mantellid Frogs from Madagascar Mol. Biol. Evol., May 1, 2008; 25(5): 874 - 891. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T.-K. Seo Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data Mol. Biol. Evol., May 1, 2008; 25(5): 960 - 971. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Larroux, G. N. Luke, P. Koopman, D. S. Rokhsar, S. M. Shimeld, and B. M. Degnan Genesis and Expansion of Metazoan Transcription Factor Gene Classes Mol. Biol. Evol., May 1, 2008; 25(5): 980 - 996. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. M. Fischer, C. W. Wheat, D. G. Heckel, and H. Vogel Evolutionary Origins of a Novel Host Plant Detoxification Gene in Butterflies Mol. Biol. Evol., May 1, 2008; 25(5): 809 - 820. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. R. Schultz and S. G. Brady From the Cover: Major evolutionary transitions in ant agriculture PNAS, April 8, 2008; 105(14): 5435 - 5440. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Nagahama, M. A. Abdel-Wahab, Y. Nogi, M. Miyazaki, K. Uematsu, M. Hamamoto, and K. Horikoshi Dipodascus tetrasporeus sp. nov., an ascosporogenous yeast isolated from deep-sea sediments in the Japan Trench Int J Syst Evol Microbiol, April 1, 2008; 58(4): 1040 - 1046. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Ehlers, G. Dural, N. Yasmum, T. Lembo, B. de Thoisy, M.-P. Ryser-Degiorgis, R. G. Ulrich, and D. J. McGeoch Novel Mammalian Herpesviruses and Lineages within the Gammaherpesvirinae: Cospeciation and Interspecies Transfer J. Virol., April 1, 2008; 82(7): 3509 - 3516. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Cadillo-Quiroz, E. Yashiro, J. B. Yavitt, and S. H. Zinder Characterization of the Archaeal Community in a Minerotrophic Fen and Terminal Restriction Fragment Length Polymorphism-Directed Isolation of a Novel Hydrogenotrophic Methanogen Appl. Envir. Microbiol., April 1, 2008; 74(7): 2059 - 2068. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. E. Valdiosera, J. L. Garcia-Garitagoitia, N. Garcia, I. Doadrio, M. G. Thomas, C. Hanni, J.-L. Arsuaga, I. Barnes, M. Hofreiter, L. Orlando, et al. From the Cover: Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos) PNAS, April 1, 2008; 105(13): 5123 - 5128. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Herde, K. Gartner, T. G. Kollner, B. Fode, W. Boland, J. Gershenzon, C. Gatz, and D. Tholl Identification and Regulation of TPS04/GES, an Arabidopsis Geranyllinalool Synthase Catalyzing the First Step in the Formation of the Insect-Induced Volatile C16-Homoterpene TMTT PLANT CELL, April 1, 2008; 20(4): 1152 - 1168. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Paape, B. Igic, S. D. Smith, R. Olmstead, L. Bohs, and J. R. Kohn A 15-Myr-Old Genetic Bottleneck Mol. Biol. Evol., April 1, 2008; 25(4): 655 - 663. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. P. Ridley, H. Y. Lee, and C. Khosla Chemical Ecology Special Feature: Evolution of polyketide synthases in bacteria PNAS, March 25, 2008; 105(12): 4595 - 4600. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Mapara, S. Parries, C. Quarrington, K.-C. Ahn, W. J. Gallin, and J. I. Goldberg Identification, molecular structure and expression of two cloned serotonin receptors from the pond snail, Helisoma trivolvis J. Exp. Biol., March 15, 2008; 211(6): 900 - 910. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Stoeck, S. Jost, and J. Boenigk Multigene phylogenies of clonal Spumella-like strains, a cryptic heterotrophic nanoflagellate, isolated from different geographical regions Int J Syst Evol Microbiol, March 1, 2008; 58(3): 716 - 724. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Wang, D. Zhan, L. Li, F. Lei, B. Liu, D. Liu, H. Xiao, Y. Feng, J. Li, B. Yang, et al. H5N1 avian influenza re-emergence of Lake Qinghai: phylogenetic and antigenic analyses of the newly isolated viruses and roles of migratory birds in virus circulation J. Gen. Virol., March 1, 2008; 89(3): 697 - 702. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. E. Horvath, D. W. Weisrock, S. L. Embry, I. Fiorentino, J. P. Balhoff, P. Kappeler, G. A. Wray, H. F. Willard, and A. D. Yoder Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar's lemurs Genome Res., March 1, 2008; 18(3): 489 - 499. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. W. Peterson Phylogenetic analysis of Aspergillus species using DNA sequences from four loci. Mycologia, March 1, 2008; 100(2): 205 - 226. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. A. Smith and C. W. Dunn Phyutility: a phyloinformatics tool for trees, alignments and molecular data Bioinformatics, March 1, 2008; 24(5): 715 - 716. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Lahaye, M. van der Bank, D. Bogarin, J. Warner, F. Pupulin, G. Gigot, O. Maurin, S. Duthoit, T. G. Barraclough, and V. Savolainen From the Cover: DNA barcoding the floras of biodiversity hotspots PNAS, February 26, 2008; 105(8): 2923 - 2928. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-C. Hon, T.-Y. Lam, Z.-L. Shi, A. J. Drummond, C.-W. Yip, F. Zeng, P.-Y. Lam, and F. C.-C. Leung Evidence of the Recombinant Origin of a Bat Severe Acute Respiratory Syndrome (SARS)-Like Coronavirus and Its Implications on the Direct Ancestor of SARS Coronavirus J. Virol., February 15, 2008; 82(4): 1819 - 1826. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. A.A. Nylander, J. C. Wilgenbusch, D. L. Warren, and D. L. Swofford AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics Bioinformatics, February 15, 2008; 24(4): 581 - 583. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. C. Opazo, F. G. Hoffmann, and J. F. Storz Genomic evidence for independent origins of {beta}-like globin genes in monotremes and therian mammals PNAS, February 5, 2008; 105(5): 1590 - 1595. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Sindhu, S. Chintamanani, A. S. Brandt, M. Zanis, S. R. Scofield, and G. S. Johal A guardian of grasses: Specific origin and conservation of a unique disease-resistance gene in the grass lineage PNAS, February 5, 2008; 105(5): 1762 - 1767. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Arai, S. N. Bennett, L. Sumibcay, J. A. Cook, J.-W. Song, A. Hope, C. Parmenter, V. R. Nerurkar, T. L. Yates, and R. Yanagihara Phylogenetically Distinct Hantaviruses in the Masked Shrew (Sorex cinereus) and Dusky Shrew (Sorex monticolus) in the United States Am J Trop Med Hyg, February 1, 2008; 78(2): 348 - 351. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. P. Fournier and J. P. Gogarten Evolution of Acetoclastic Methanogenesis in Methanosarcina via Horizontal Gene Transfer from Cellulolytic Clostridia J. Bacteriol., February 1, 2008; 190(3): 1124 - 1127. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Zidi, A. Sanchez, G. Obexer-Ruff, and M. Amills Sequence Analysis of Goat Major Histocompatibility Complex Class I Genes J Dairy Sci, February 1, 2008; 91(2): 814 - 817. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Nikoh, K. Tanaka, F. Shibata, N. Kondo, M. Hizume, M. Shimada, and T. Fukatsu Wolbachia genome integrated in an insect chromosome: Evolution and fate of laterally transferred endosymbiont genes Genome Res., February 1, 2008; 18(2): 272 - 280. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. W. Grimm and T. Denk ITS Evolution in Platanus (Platanaceae): Homoeologues, Pseudogenes and Ancient Hybridization Ann. Bot., February 1, 2008; 101(3): 403 - 419. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. S. Devey, R. M. Bateman, M. F. Fay, and J. A. Hawkins Friends or Relatives? Phylogenetics and Species Delimitation in the Controversial European Orchid Genus Ophrys Ann. Bot., February 1, 2008; 101(3): 385 - 402. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. J. Salipante, J. M. Thompson, and M. S. Horwitz Phylogenetic Fate Mapping: Theoretical and Experimental Studies Applied to the Development of Mouse Fibroblasts Genetics, February 1, 2008; 178(2): 967 - 977. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. M. Matzkin The Molecular Basis of Host Adaptation in Cactophilic Drosophila: Molecular Evolution of a Glutathione S-Transferase Gene (GstD1) in Drosophila mojavensis Genetics, February 1, 2008; 178(2): 1073 - 1083. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. A. Ayoub and C. Y. Hayashi Multiple Recombining Loci Encode MaSp1, the Primary Constituent of Dragline Silk, in Widow Spiders (Latrodectus: Theridiidae) Mol. Biol. Evol., February 1, 2008; 25(2): 277 - |