Molecular Biology and Evolution

MBE Advance Access published online on May 7, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm092

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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Letter

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

Koichiro Tamura^1,2, Joel Dudley¹, Masatoshi Nei³ and Sudhir Kumar^1,4,*

¹ Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA
² Department of Biological Sciences, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192-0397, Japan
³ Department of Biology and the Institute of Molecular Evolutionary Genetics, The Pennsylvania State University, University Park, PA 16802, USA
⁴ School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA

^* Address for Correspondence: Sudhir Kumar, Biodesign Institute Building A240, Arizona State University, 1001 S. McAllister Avenue, Tempe, AZ 85287-5301, Tel: 480-727-6949, E-mail: s.kumar{at}asu.edu

Received for publication March 22, 2007. Revision received April 26, 2007. Accepted for publication May 2, 2007.

We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from auto-sequencers, mining web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pair of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without the knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current test version of MEGA is available free of charge at http://www.megasoftware.net.

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				J. Schafer, H.-J. Busse, and P. Kampfer Pseudonocardia parietis sp. nov., from the indoor environment Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2449 - 2452. [Abstract] [Full Text] [PDF]

				Y.-P. Xiao, W. Hui, Q. Wang, S. W. Roh, X.-Q. Shi, J.-H. Shi, and Z.-X. Quan Pseudomonas caeni sp. nov., a denitrifying bacterium isolated from the sludge of an anaerobic ammonium-oxidizing bioreactor Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2594 - 2598. [Abstract] [Full Text] [PDF]

				Y. Zhao, W. Wei, I.-M. Lee, J. Shao, X. Suo, and R. E. Davis Construction of an interactive online phytoplasma classification tool, iPhyClassifier, and its application in analysis of the peach X-disease phytoplasma group (16SrIII) Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2582 - 2593. [Abstract] [Full Text] [PDF]

				Y.-G. Chen, Y.-Q. Zhang, Z.-X. Liu, D.-C. Zhuang, H.-P. Klenk, S.-K. Tang, X.-L. Cui, and W.-J. Li Halobacillus salsuginis sp. nov., a moderately halophilic bacterium from a subterranean brine Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2505 - 2509. [Abstract] [Full Text] [PDF]

				J.-H. Chou, Y.-J. Chou, A. B. Arun, C.-C. Young, C. A. Chen, J.-T. Wang, and W.-M. Chen Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond Int J Syst Evol Microbiol, October 1, 2009; 59(10): 2629 - 2632. [Abstract] [Full Text] [PDF]

				M. A. Mullins, K. B. Register, D. O. Bayles, C. L. Loving, T. L. Nicholson, S. L. Brockmeier, D. W. Dyer, and G. J. Phillips Characterization and Comparative Analysis of the Genes Encoding Haemophilus parasuis Outer Membrane Proteins P2 and P5 J. Bacteriol., October 1, 2009; 191(19): 5988 - 6002. [Abstract] [Full Text] [PDF]

				H. Nakayama-Imaohji, H. Hirakawa, M. Ichimura, S. Wakimoto, S. Kuhara, T. Hayashi, and T. Kuwahara Identification of the Site-Specific DNA Invertase Responsible for the Phase Variation of SusC/SusD Family Outer Membrane Proteins in Bacteroides fragilis J. Bacteriol., October 1, 2009; 191(19): 6003 - 6011. [Abstract] [Full Text] [PDF]

				P. E. Carter, S. M. McTavish, H. J. L. Brooks, D. Campbell, J. M. Collins-Emerson, A. C. Midwinter, and N. P. French Novel Clonal Complexes with an Unknown Animal Reservoir Dominate Campylobacter jejuni Isolates from River Water in New Zealand Appl. Envir. Microbiol., October 1, 2009; 75(19): 6038 - 6046. [Abstract] [Full Text] [PDF]

				M. V. Rodrigues, N. Borges, C. P. Almeida, P. Lamosa, and H. Santos A Unique {beta}-1,2-Mannosyltransferase of Thermotoga maritima That Uses Di-myo-Inositol Phosphate as the Mannosyl Acceptor J. Bacteriol., October 1, 2009; 191(19): 6105 - 6115. [Abstract] [Full Text] [PDF]

				A. Low, N. Prada, M. Topper, F. Vaida, D. Castor, H. Mohri, D. Hazuda, M. Muesing, and M. Markowitz Natural Polymorphisms of Human Immunodeficiency Virus Type 1 Integrase and Inherent Susceptibilities to a Panel of Integrase Inhibitors Antimicrob. Agents Chemother., October 1, 2009; 53(10): 4275 - 4282. [Abstract] [Full Text] [PDF]

				C. X. Machado, P. M. Pinto, A. Zaha, and H. B. Ferreira A peroxiredoxin from Mycoplasma hyopneumoniae with a possible role in H2O2 detoxification Microbiology, October 1, 2009; 155(10): 3411 - 3419. [Abstract] [Full Text] [PDF]

				R. Begum, S. S. Alam, G. Menzel, and T. Schmidt Comparative molecular cytogenetics of major repetitive sequence families of three Dendrobium species (Orchidaceae) from Bangladesh Ann. Bot., October 1, 2009; 104(5): 863 - 872. [Abstract] [Full Text] [PDF]

				M. C. Voicu, J. E. K. Cooke, and J. J. Zwiazek Aquaporin gene expression and apoplastic water flow in bur oak (Quercus macrocarpa) leaves in relation to the light response of leaf hydraulic conductance J. Exp. Bot., October 1, 2009; 60(14): 4063 - 4075. [Abstract] [Full Text] [PDF]

				S. Gowtage-Sequeira, A. C. Banyard, T. Barrett, H. Buczkowski, S. M. Funk, and S. Cleaveland EPIDEMIOLOGY, PATHOLOGY, AND GENETIC ANALYSIS OF A CANINE DISTEMPER EPIDEMIC IN NAMIBIA J. Wildl. Dis., October 1, 2009; 45(4): 1008 - 1020. [Abstract] [Full Text] [PDF]

				M. W. Cunningham, D. B. Shindle, A. B. Allison, S. P. Terrell, D. G. Mead, and M. Owen Canine Distemper Epizootic in Everglades Mink J. Wildl. Dis., October 1, 2009; 45(4): 1150 - 1157. [Abstract] [Full Text] [PDF]

				D. S. Smyth, E. J. Feil, W. J. Meaney, P. J. Hartigan, T. Tollersrud, J. R. Fitzgerald, M. C. Enright, and C. J. Smyth Molecular genetic typing reveals further insights into the diversity of animal-associated Staphylococcus aureus J. Med. Microbiol., October 1, 2009; 58(10): 1343 - 1353. [Abstract] [Full Text] [PDF]

				S. Chattopadhyay, R. N. Paranjpye, D. E. Dykhuizen, E. V. Sokurenko, and M. S. Strom Comparative Evolutionary Analysis of the Major Structural Subunit of Vibrio vulnificus Type IV Pili Mol. Biol. Evol., October 1, 2009; 26(10): 2185 - 2196. [Abstract] [Full Text] [PDF]

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