Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S.. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 28: 2731-2739

Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
Molecular Biology and Evolution (Impact Factor: 9.11). 05/2011; 28(10):2731-9. DOI: 10.1093/molbev/msr121
Source: PubMed

ABSTRACT Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from

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Available from: Masatoshi Nei, Sep 27, 2015
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    • "phylogeny was established on a subset of species (ca 40%) using nucleotide sequence data for the rbcL gene extracted from the Gen- Bank database. This phylogeny was obtained using the BEAST 1.7 software (Drummond et al., 2012) after alignment of the sequences in Mega 5.1 (Tamura et al., 2011). This first tree was compared according to APG3 to check for misidentification in published sequences. "
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    Ecological Indicators 01/2016; 60:736-745. DOI:10.1016/j.ecolind.2015.07.017 · 3.44 Impact Factor
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    • "(Hall 1999) and aligned using CLUSTAL_X 1.83 (Thompson et al. 1997) and MEGA 5.2.2 (Tamura et al. 2011). Phylogenetic relationships among sequences were reconstructed for each gene separately using maximumlikelihood in the program MEGA 5.2.2 (Tamura et al. 2011). The most appropriate substitution model was determined using BIC as implemented in jModel Test 2.14 (Darriba et al. 2012). "
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    ABSTRACT: Rhinolophus affinis sensu lato is distributed throughout Southeast Asia. The taxonomic status of forms attributed to the species is unclear due to the limited sample size with incomplete datasets and the taxa have high variation in morphology and echolocation call frequency. The aim of the study was to evaluate the distribution and taxonomic status of the subspecific forms of R. affinis in mainland Southeast Asia using large sample size with multiple datasets, including morphological, acoustic, and genetic data, both to elucidate taxonomic relationships and to test for congruence between these datasets. Three morphological forms were confirmed within the region; two concur with previously recognized taxa, namely R. affinis macrurus and R. affinis superans, and are strongly supported by morphological and genetic data. The third form is morphologically distinct, but its taxonomic status remains unclear. It is probable that this third form represents a distinct taxonomic entity; however, more data are required to confirm this. R. a. macrurus is known from the north of peninsular Thailand, Cambodia, Myanmar, Laos, and Vietnam (Indochinese subregion); R. a. superans is found throughout the Thai-Malay Peninsula (Sundaic subregion); whilst the third form is presently known from east central Myanmar (Shan state) and lower northern Vietnam (Nghe An Province). Our results suggest that at least three morphological forms occur in mainland Southeast Asia including one form which appears to be new to science. Echolocation call data for R. affinis are not a robust taxonomic tool as it shows a significant degree of variation which is not explained or supported by genetic and morphological findings. This study highlights significant levels of morphological variation in mainland Southeast Asia and provides an essential basis for further studies aiming to understand the population genetics, phylogeography, and taxonomy of the species.
    12/2015; 54(1). DOI:10.1186/s40555-015-0109-8
    • "The obtained sequences were edited using FinchTV v. 1.4.0 ( and assembled using the Clustal W program integrated into MEGA 5.2 software (Tamura et al., 2011). For all genomic loci, the sequences were aligned with reference strains of the 16SrIII phytoplasma group (Zhao et al., 2009; Amaral Mello et al., 2011; Davis et al., 2013; Galdeano et al., 2013; Lee et al., 2014) that were retrieved online from the National Center for Biotechnology Information ( and used to construct phylogenetic trees. "
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    Annals of Applied Biology 11/2015; DOI:10.1111/aab.12236 · 2.00 Impact Factor
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