MBE Advance Access originally published online on May 7, 2007
Molecular Biology and Evolution 2007 24(8):1596-1599; doi:10.1093/molbev/msm092
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MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0
,*
* Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University
Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
Department of Biology and the Institute of Molecular Evolutionary Genetics, The Pennsylvania State University
School of Life Sciences, Arizona State University
E-mail: s.kumar{at}asu.edu
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 autosequencers, 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 pairs 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 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 version of MEGA is available free of charge at http://www.megasoftware.net.
Key Words: selection • genomics • phylogenetics • software • cross-platform
William Martin, Associate Editor
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 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]
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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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D.-D. Wu, G.-D. Wang, D. M Irwin, and Y.-P. Zhang A Profound Role for the Expansion of Trypsin-Like Serine Protease Family in the Evolution of Hematophagy in Mosquito Mol. Biol. Evol., October 1, 2009; 26(10): 2333 - 2341. [Abstract] [Full Text] [PDF]
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W. A. Vargas, J. C. Mandawe, and C. M. Kenerley Plant-Derived Sucrose Is a Key Element in the Symbiotic Association between Trichoderma virens and Maize Plants Plant Physiology, October 1, 2009; 151(2): 792 - 808. [Abstract] [Full Text] [PDF]
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M. Novo, F. Bigey, E. Beyne, V. Galeote, F. Gavory, S. Mallet, B. Cambon, J.-L. Legras, P. Wincker, S. Casaregola, et al. Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118 PNAS, September 22, 2009; 106(38): 16333 - 16338. [Abstract] [Full Text] [PDF]
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M. Jalasvuori, S. T. Jaatinen, S. Laurinavicius, E. Ahola-Iivarinen, N. Kalkkinen, D. H. Bamford, and J. K. H. Bamford The Closest Relatives of Icosahedral Viruses of Thermophilic Bacteria Are among Viruses and Plasmids of the Halophilic Archaea J. Virol., September 15, 2009; 83(18): 9388 - 9397. [Abstract] [Full Text] [PDF]
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F. Fang, Y. Li, M. Bumann, E. J. Raftis, P. G. Casey, J. C. Cooney, M. A. Walsh, and P. W. O'Toole Allelic Variation of Bile Salt Hydrolase Genes in Lactobacillus salivarius Does Not Determine Bile Resistance Levels J. Bacteriol., September 15, 2009; 191(18): 5743 - 5757. [Abstract] [Full Text] [PDF]
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J. van Ingen, R. de Zwaan, R. Dekhuijzen, M. Boeree, and D. van Soolingen Region of Difference 1 in Nontuberculous Mycobacterium Species Adds a Phylogenetic and Taxonomical Character J. Bacteriol., September 15, 2009; 191(18): 5865 - 5867. [Abstract] [Full Text] [PDF]
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K. Liu, S. J. Knabel, and E. G. Dudley rhs Genes Are Potential Markers for Multilocus Sequence Typing of Escherichia coli O157:H7 Strains Appl. Envir. Microbiol., September 15, 2009; 75(18): 5853 - 5862. [Abstract] [Full Text] [PDF]
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 Z. Xia, G. Jin, J. Zhu, and R. Zhou Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus Bioinformatics, September 15, 2009; 25(18): 2309 - 2317. [Abstract] [Full Text] [PDF]
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L. Cavinta, G. Cao, and S. Schaefer Description of a New Hepatitis B Virus C6 Subgenotype Found in the Papua Province of Indonesia and Suggested Renaming of a Tentative C6 Subgenotype Found in the Philippines as Subgenotype C7 J. Clin. Microbiol., September 1, 2009; 47(9): 3068 - 3069. [Full Text] [PDF]
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 M. L. Beeton, V. J. Chalker, S. Kotecha, and O. B. Spiller Comparison of full gyrA, gyrB, parC and parE gene sequences between all Ureaplasma parvum and Ureaplasma urealyticum serovars to separate true fluoroquinolone antibiotic resistance mutations from non-resistance polymorphism J. Antimicrob. Chemother., September 1, 2009; 64(3): 529 - 538. [Abstract] [Full Text] [PDF]
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 P. Schwarz, P. Strnad, N. Singer, F. Oswald, R. Ehehalt, G. Adler, and H. Kulaksiz Identification, sequencing, and cellular localization of hepcidin in guinea pig (Cavia porcellus) J. Endocrinol., September 1, 2009; 202(3): 389 - 396. [Abstract] [Full Text] [PDF]
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S. C. Leao, E. Tortoli, C. Viana-Niero, S. Y. M. Ueki, K. V. B. Lima, M. L. Lopes, J. Yubero, M. C. Menendez, and M. J. Garcia Characterization of Mycobacteria from a Major Brazilian Outbreak Suggests that Revision of the Taxonomic Status of Members of the Mycobacterium chelonae-M. abscessus Group Is Needed J. Clin. Microbiol., September 1, 2009; 47(9): 2691 - 2698. [Abstract] [Full Text] [PDF]
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 A. M. Buboltz, T. L. Nicholson, L. S. Weyrich, and E. T. Harvill Role of the Type III Secretion System in a Hypervirulent Lineage of Bordetella bronchiseptica Infect. Immun., September 1, 2009; 77(9): 3969 - 3977. [Abstract] [Full Text] [PDF]
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C. Y. Hwang and B. C. Cho Spongiibacter tropicus sp. nov., isolated from a Synechococcus culture Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2176 - 2179. [Abstract] [Full Text] [PDF]
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S.-K. Tang, Y. Wang, J.-Y. Wu, L.-L. Cao, K. Lou, L.-H. Xu, C.-L. Jiang, and W.-J. Li Saccharopolyspora qijiaojingensis sp. nov., a halophilic actinomycete isolated from a salt lake Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2166 - 2170. [Abstract] [Full Text] [PDF]
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M. Al Masalma, D. Raoult, and V. Roux Phocaeicola abscessus gen. nov., sp. nov., an anaerobic bacterium isolated from a human brain abscess sample Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2232 - 2237. [Abstract] [Full Text] [PDF]
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Z.-L. Liao, S.-K. Tang, L. Guo, Y.-Q. Zhang, X.-P. Tian, C.-L. Jiang, L.-H. Xu, and W.-J. Li Verrucosispora lutea sp. nov., isolated from a mangrove sediment sample Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2269 - 2273. [Abstract] [Full Text] [PDF]
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E. V. Pikuta, R. B. Hoover, D. Marsic, W. B. Whitman, B. Lupa, J. Tang, and P. Krader Proteocatella sphenisci gen. nov., sp. nov., a psychrotolerant, spore-forming anaerobe isolated from penguin guano Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2302 - 2307. [Abstract] [Full Text] [PDF]
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J. van Ingen, M. J. Boeree, K. Kosters, A. Wieland, E. Tortoli, P. N. R. Dekhuijzen, and D. van Soolingen Proposal to elevate Mycobacterium avium complex ITS sequevar MAC-Q to Mycobacterium vulneris sp. nov. Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2277 - 2282. [Abstract] [Full Text] [PDF]
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M.-S. Kim, S. W. Roh, Y.-D. Nam, H.-W. Chang, K.-H. Kim, M.-J. Jung, J.-H. Choi, E.-J. Park, and J.-W. Bae Alishewanella jeotgali sp. nov., isolated from traditional fermented food, and emended description of the genus Alishewanella Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2313 - 2316. [Abstract] [Full Text] [PDF]
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