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

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Tamura, K., Dudley, J., Nei, M., Kumar, S.·2007·Molecular Biology and Evolution

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Abstract

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).

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“Phylogenetic tree of protein clusters from various species was constructed by neighborjoining (NJ) method using software MEGA 5 [20].”
Method
Altered carbohydrate metabolism in the storage roots of sweetpotato plants overexpressing the SRF1 gene, which encodes a Dof zinc finger transcription factor
Tanaka, M., Takahata, Y., Nakayama, H., Nakatani, M., & Tahara, M. (2009) · Planta · doi:10.1007/s00425-009-0979-2 · Cited by 106
Recombinational Switching of the Clostridium difficile S-Layer and a Novel Glycosylation Gene Cluster Revealed by Large-Scale Whole-Genome Sequencing
Dingle, K. E., Didelot, X., Ansari, M. A., Eyre, D. W., Vaughan, A., Griffiths, D., Ip, C. L. C., Batty, E. M., Golubchik, T., Bowden, R., et al. (2013) · The Journal of Infectious Diseases · doi:10.1093/infdis/jis734 · Cited by 104
Genome-wide analysis of the LEA (late embryogenesis abundant) protein gene family in Populus trichocarpa
Lan, T., Gao, J., & Zeng, Q.-Y. (2013) · Tree Genetics & Genomes · doi:10.1007/s11295-012-0551-2 · Cited by 102
Vertebrate ancient opsin and melanopsin: divergent irradiance detectors
Davies, W. L., Hankins, M. W., & Foster, R. G. (2010) · Photochemical & Photobiological Sciences · doi:10.1039/c0pp00203h · Cited by 100
Putrescine N-methyltransferase – The start for alkaloids
Biastoff, S., Brandt, W., & Dräger, B. (2009) · Phytochemistry · doi:10.1016/j.phytochem.2009.06.012 · Cited by 87
Over-expression of a tomato N-acetyl-L-glutamate synthase gene (SlNAGS1) in Arabidopsis thaliana results in high ornithine levels and increased tolerance in salt and drought stresses
Kalamaki, M. S., Alexandrou, D., Lazari, D., Merkouropoulos, G., Fotopoulos, V., Pateraki, I., Aggelis, A., Carrillo-López, A., Rubio-Cabetas, M. J., & Kanellis, A. K. (2009) · Journal of Experimental Botany · doi:10.1093/jxb/erp072 · Cited by 97
Neurexin-Neuroligin Transsynaptic Interaction Mediates Learning-Related Synaptic Remodeling and Long-Term Facilitation in Aplysia
Choi, Y.-B., Li, H.-L., Kassabov, S. R., Jin, I., Puthanveettil, S. V., Karl, K. A., Lu, Y., Kim, J.-H., Bailey, C. H., & Kandel, E. R. (2011) · Neuron · doi:10.1016/j.neuron.2011.03.020 · Cited by 94
Identification and Antimicrobial Activity Detection of Lactic Acid Bacteria Isolated from Corn Stover Silage
Li, D., Ni, K., Pang, H., Wang, Y., Cai, Y., & Jin, Q. (2015) · Asian-Australasian Journal of Animal Sciences · doi:10.5713/ajas.14.0439 · Cited by 92
Cryptic biodiversity in streams: a comparison of macroinvertebrate communities based on morphological and DNA barcode identifications
Jackson, J. K., Battle, J. M., White, B. P., Pilgrim, E. M., Stein, E. D., Miller, P. E., & Sweeney, B. W. (2014) · Freshwater Science · doi:10.1086/675225 · Cited by 91
Highly diversified innate receptor systems and new forms of animal immunity
Messier-Solek, C., Buckley, K. M., & Rast, J. P. (2010) · Seminars in Immunology · doi:10.1016/j.smim.2009.11.007 · Cited by 87
A Novel Metal Transporter Mediating Manganese Export (MntX) Regulates the Mn to Fe Intracellular Ratio and Neisseria meningitidis Virulence
Veyrier, F. J., Boneca, I. G., Cellier, M. F., & Taha, M.-K. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002261 · Cited by 85
SNPs in Genes Functional in Starch-Sugar Interconversion Associate with Natural Variation of Tuber Starch and Sugar Content of Potato (Solanum tuberosum L.)
Schreiber, L., Nader-Nieto, A. C., Schönhals, E. M., Walkemeier, B., & Gebhardt, C. (2014) · G3 Genes|Genomes|Genetics · doi:10.1534/g3.114.012377 · Cited by 81
Community profiling and gene expression of fungal assimilatory nitrate reductases in agricultural soil
Gorfer, M., Blumhoff, M., Klaubauf, S., Urban, A., Inselsbacher, E., Bandian, D., Mitter, B., Sessitsch, A., Wanek, W., & Strauss, J. (2011) · The ISME Journal · doi:10.1038/ismej.2011.53 · Cited by 78
Elucidating the spread of the emerging canid nematode Angiostrongylus vasorum between Palaearctic and Nearctic ecozones
Jefferies, R., Shaw, S. E., Willesen, J., Viney, M. E., & Morgan, E. R. (2010) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2010.01.013 · Cited by 78
Mollusc gonadotropin-releasing hormone directly regulates gonadal functions: A primitive endocrine system controlling reproduction
Treen, N., Itoh, N., Miura, H., Kikuchi, I., Ueda, T., Takahashi, K. G., Ubuka, T., Yamamoto, K., Sharp, P. J., Tsutsui, K., et al. (2012) · General and Comparative Endocrinology · doi:10.1016/j.ygcen.2012.01.008 · Cited by 77
A functional pectin methylesterase inhibitor protein (SolyPMEI) is expressed during tomato fruit ripening and interacts with PME-1
Reca, I. B., Lionetti, V., Camardella, L., D’Avino, R., Giardina, T., Cervone, F., & Bellincampi, D. (2012) · Plant Molecular Biology · doi:10.1007/s11103-012-9921-2 · Cited by 76
Molecular Epidemiology of Human Enterovirus Associated with Aseptic Meningitis in Shandong Province, China, 2006–2012
Tao, Z., Wang, H., Li, Y., Liu, G., Xu, A., Lin, X., Song, L., Ji, F., Wang, S., Cui, N., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0089766 · Cited by 71
“0 [16] using neighbor-joining method after estimation of genetic distance using the Kimura two-parameter method [17].”
Method
Anti-lipopolysaccharide factors in the American lobster Homarus americanus: Molecular characterization and transcriptional response to Vibrio fluvialis challenge
Beale, K. M., Towle, D. W., Jayasundara, N., Smith, C. M., Shields, J. D., Small, H. J., & Greenwood, S. J. (2008) · Comparative Biochemistry and Physiology Part D: Genomics and Proteomics · doi:10.1016/j.cbd.2008.07.001 · Cited by 72
Patterns and processes of diversification in a widespread and ecologically diverse avian group, the buteonine hawks (Aves, Accipitridae)
do Amaral, F. R., Sheldon, F. H., Gamauf, A., Haring, E., Riesing, M., Silveira, L. F., & Wajntal, A. (2009) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.07.020 · Cited by 69
Multiple determinants within iron-responsive elements dictate iron regulatory protein binding and regulatory hierarchy
Goforth, J. B., Anderson, S. A., Nizzi, C. P., & Eisenstein, R. S. (2010) · RNA · doi:10.1261/rna.1857210 · Cited by 71
Mechanisms of genetic variation in polioviruses
Savolainen‐Kopra, C., & Blomqvist, S. (2010) · Reviews in Medical Virology · doi:10.1002/rmv.663 · Cited by 67
SslE Elicits Functional Antibodies That Impair In Vitro Mucinase Activity and In Vivo Colonization by Both Intestinal and Extraintestinal Escherichia coli Strains
Nesta, B., Valeri, M., Spagnuolo, A., Rosini, R., Mora, M., Donato, P., Alteri, C. J., Del Vecchio, M., Buccato, S., Pezzicoli, A., et al. (2014) · PLoS Pathogens · doi:10.1371/journal.ppat.1004124 · Cited by 68
Exploring a blue-light-sensing transcription factor to double the peak productivity of oil in Nannochloropsis oceanica
Zhang, P., Xin, Y., He, Y., Tang, X., Shen, C., Wang, Q., Lv, N., Li, Y., Hu, Q., & Xu, J. (2022) · Nature Communications · doi:10.1038/s41467-022-29337-x · Cited by 67

Authors: Tamura, K., Dudley, J., Nei, M., & Kumar, S.
Venue: Molecular Biology and Evolution
Publisher: Oxford University Press (OUP)
Published: 2007-04-18
Volume: 24
Issue: 8
Pages: 1596-1599
ISSN: 0737-4038 (ISSN-L)
1537-1719
DOI: 10.1093/molbev/msm092
OpenAlex: W2125121305
Cited by: 28,730
References: 0
FWCI: 1014.47
Type: journal article
Language: en
Open access: bronze

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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.

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

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