MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, And Maximum Parsimony Methods

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


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
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    • ".com/primerdesign/index.html)[27]. Genotyping of HBV was then performed by phylogenetically analyzing the S gene using sequences from the data- base[42]. "
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    ABSTRACT: Background: In occult hepatitis B viral infection (OBI), the persistence of hepatitis B virus (HBV) DNA is associated with a lack of hepatitis B surface antigen (HBsAg). To assess the possible role of HBsAg immune escape variants in OBI patients, variability in the HBV S gene was evaluated for OBI patients as well as chronic HBV infection patients from the same families. Methods: We selected 17 HBV DNA-positive/HBsAg-negative patients (OBI group) and 15 HBV DNA- and HBsAg-positive patients from OBI families (control group). The S gene was amplified and cloned, and at least 15 clones per patient were sequenced and analyzed. Results: Although the incidence of stop codon mutations within the S region was higher in the OBI group (13.6 %) than in the control group (1.5 %, P < 0.001), this type of mutation, together with insertion and deletion mutations, was prevalent in only three OBI patients. In the major hydrophilic region (MHR), a median of 0.75 residues were altered in every 100 residues for the OBI patients, whereas 0.95 out of 100 residues were changed in the control group (P = 0.428). Furthermore, some variants that are generally considered immune escape variants, such as mutations at positions s145, s147, and s123, were only observed in less than 5 % of all the clones sequenced, in either OBI or control group. Conclusions: Our data suggest that HBsAg variants may not play a major role in OBI pathogenesis.
    Preview · Article · Dec 2016 · Virology Journal
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    • "The alignment was trimmed manually in BioEdit[106]. A maximum likelihood tree was built using MEGA version 5.2[107]. The Jones- Taylor-Thornton (JTT) amino acid substitution matrix was used and 150 bootstrap iterations were used to obtain support values at each node. "
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    ABSTRACT: Background The cranial sensory ganglia represent populations of neurons with distinct functions, or sensory modalities. The production of individual ganglia from distinct neurogenic placodes with different developmental pathways provides a powerful model to investigate the acquisition of specific sensory modalities. To date there is a limited range of gene markers available to examine the molecular pathways underlying this process. Results Transcriptional profiles were generated for populations of differentiated neurons purified from distinct cranial sensory ganglia using microdissection in embryonic chicken followed by FAC-sorting and RNAseq. Whole transcriptome analysis confirmed the division into somato- versus viscerosensory neurons, with additional evidence for subdivision of the somatic class into general and special somatosensory neurons. Cross-comparison of distinct ganglia transcriptomes identified a total of 134 markers, 113 of which are novel, which can be used to distinguish trigeminal, vestibulo-acoustic and epibranchial neuronal populations. In situ hybridisation analysis provided validation for 20/26 tested markers, and showed related expression in the target region of the hindbrain in many cases. Conclusions One hundred thirty-four high-confidence markers have been identified for placode-derived cranial sensory ganglia which can now be used to address the acquisition of specific cranial sensory modalities. Electronic supplementary material The online version of this article (doi:10.1186/s13064-016-0057-y) contains supplementary material, which is available to authorized users.
    Full-text · Article · Dec 2016 · Neural Development
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    • "The two parameters H' and S were estimated with the function diversity in the package vegan[36]. To calculate GD, we estimated pairwise genetic distances of the mitochondrial 16S rRNA sequences of prey species with the Tamura-Nei[37]+ G distance model and complete deletion of gaps in MEGA 5.05[38], and computed the average genetic distances. We performed sliding-window analyses of H' , S and GD of dietary compositions with a window size of 5 mm in shell lengths. "
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    Full-text · Article · Dec 2016 · BMC Evolutionary Biology
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