We announce the release of an advanced version Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In 6.0, MEGA now enables inference timetrees, as it implements RelTime method estimating divergence times all branching points in a phylogeny. A new Timetree Wizard MEGA6 facilitates this timetree by providing graphical user interface...

Abstract We present the latest version of Molecular Evolutionary Genetics Analysis (M ega ) software, which contains many sophisticated methods and tools for phylogenomics phylomedicine. In this major upgrade, M has been optimized use on 64-bit computing systems analyzing larger datasets. Researchers can now explore analyze tens thousands sequences in . The new also provides an advanced wizard building timetrees includes a functionality to automatically predict gene duplication events family...

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories species and inferring nature extent selective forces shaping evolution genes species. Here, we announce release Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which a user-friendly software mining online databases, building alignments phylogenetic trees, using methods bioinformatics in basic biology, biomedicine, evolution. The newest addition MEGA5 collection maximum...

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows Linux operating systems. X does not require virtualization or emulation provides uniform user experience across platforms. has additionally been upgraded multiple computing cores molecular evolutionary analyses. is available in two interfaces (graphical command...

We announce the release of fourth version MEGA software, which expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual alignment, analyzing alignments to estimate evolutionary distances, inferring phylogenetic trees, testing hypotheses. Version 4 includes a unique facility generate captions, written in figure legend format, order provide natural language descriptions models methods used analyses. This aims...

The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools computational molecular evolution. Here, we describe new additions that make MEGA more comprehensive tool for building timetrees species, pathogens, gene families using rapid relaxed-clock methods. Methods estimating divergence times confidence intervals are implemented use probability densities calibration constraints node-dating sequence sampling dates tip-dating...

With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA protein sequence analysis plays a central role reconstructing histories of species multigene families, estimating rates evolution, inferring nature extent selective forces shaping evolution genes genomes. The scope these investigations has now expanded greatly owing to development high-throughput sequencing techniques novel statistical computational methods. These methods...

Examining the pattern of nucleotide substitution for control region mitochondrial DNA (mtDNA) in humans and chimpanzees, we developed a new mathematical method estimating number transitional transversional substitutions per site, as well total substitutions. In this method, excess transitions, unequal frequencies, variation rate among different sites are all taken into account. Application to human chimpanzee data suggested that transition/transversion ratio entire was approximately 15...

Abstract Summary: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA 1 by: (1) facilitating analyses large datasets; (2) enabling creation groups sequences; (3) specification domains genes; (4) expanding repertoire statistical methods molecular studies; (5) adding modules visual representation input...

Current efforts to reconstruct the tree of life and histories multigene families demand inference phylogenies consisting thousands gene sequences. However, for such large data sets even a moderate exploration space needed identify optimal is virtually impossible. For these cases neighbor-joining (NJ) method frequently used because its demonstrated accuracy smaller computational speed. As grow, however, fraction examined by NJ algorithm becomes minuscule. Here, we report results our computer...

The Molecular Evolutionary Genetics Analysis (MEGA) software is a desktop application designed for comparative analysis of homologous gene sequences either from multigene families or different species with special emphasis on inferring evolutionary relationships and patterns DNA protein evolution. In addition to the tools statistical data, MEGA provides many convenient facilities assembly sequence data sets files web-based repositories, it includes visual presentation results obtained in...

A simple mathematical method is developed to estimate the number of nucleotide substitutions per site between two DNA sequences, by extending Kimura's (1980) two-parameter case where a G+C-content bias exists. This will be useful when there are strong transition-transversion and biases, as in Drosophila mitochondrial DNA.

Abstract The Molecular Evolutionary Genetics Analysis (MEGA) software enables comparative analysis of molecular sequences in phylogenetics and evolutionary medicine. Here, we introduce the macOS version MEGA software. This new eliminates need for virtualization emulation programs previously required to use on Apple computers. utilizes memory computing resources efficiently conducting analyses macOS. It has a native Cocoa graphical user interface that is programmed provide consistent...

A computer program package called MEGA has been developed for estimating evolutionary distances, reconstructing phylogenetic trees and computing basic statistical quantities from molecular data. It is written in C++ intended to be used on IBM IBM-compatible personal computers. In this program, various methods distances nucleotide amino acid sequence data, three different of inference (UPGMA, neighbor-joining maximum parsimony) two tests topological differences are included. For the parsimony...

Molecular dating of species divergences has become an important means to add a temporal dimension the Tree Life. Increasingly larger datasets encompassing greater taxonomic diversity are becoming available generate molecular timetrees by using sophisticated methods that model rate variation among lineages. However, practical application these is challenging because exorbitant calculation times required current for contemporary data sizes, difficulty in correctly modeling heterogeneity highly...

Drosophila melanogaster has been a canonical model organism to study genetics, development, behavior, physiology, evolution, and population genetics for nearly century. Despite this emphasis the completion of its nuclear genome sequence, timing major speciation events leading origin fruit fly remain elusive because paucity extensive fossil records biogeographic data. Use molecular clocks as an alternative fraught with non-clock-like accumulation nucleotide amino-acid substitutions. Here we...

Abstract Summary: There is a growing need in the research community to apply molecular evolutionary genetics analysis (MEGA) software tool for batch processing large number of datasets and integrate it into workflows. Therefore, we now make available computing core MEGA as stand-alone executable (MEGA-CC), along with an prototyper (MEGA-Proto). MEGA-CC provides users access all computational analyses through MEGA’s graphical user interface version. This includes methods multiple sequence...

RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in phylogeny. It shows excellent performance estimating for both simulated and empirical sequence data sets which evolutionary rates varied extensively throughout tree. is computationally efficient scales well with increasing size sets. Until now, however, has not had formal mathematical foundation. Here, we show that basis approach relative rate framework (RRF) combines comparisons sister lineages...

Abstract We introduce the 12th version of Molecular Evolutionary Genetics Analysis (MEGA12) software. This latest brings many significant improvements by reducing computational time needed for selecting optimal substitution models and conducting bootstrap tests on phylogenies using maximum likelihood (ML) methods. These are achieved implementing heuristics that minimize likely unnecessary computations. Analyses empirical simulated datasets show substantial savings these without compromising...

Most of the sophisticated methods to estimate evolutionary divergence between DNA sequences assume that two have evolved with same pattern nucleotide substitution after their from most recent common ancestor (homogeneity assumption). If this assumption is violated, distance estimated will be biased, which may result in biased estimates times and rates, lead erroneous branching patterns inferred phylogenies. Here we present a simple modification for existing estimation relax homogeneity among...

The precise position of the replication origin (O(R)) mtDNA was determined for insect species belonging to four different orders (four Drosophila, Bombyx mori, Triborium castaneum, and Locusta migratoria, which belong Diptera, Lepidoptera, Coleoptera, Orthoptera, respectively). Since free 5' ends DNA strands are interpreted as O(R), their positions were mapped at 1-nucleotide resolution within A + T-rich region by using ligation-mediated PCR method. In all examined, found a very narrow range...

Seventy-four patients were treated with a radical or nonradical pancreatectomy for ductal cell carcinoma of the head pancreas. Their survival rates and selection operative procedure evaluated. In 32 patients, was attempted where there sufficient clearance regional juxta-regional lymph nodes beyond group suspected metastatic nodes, as well resection greater margin soft tissue around These patients' cumulative 5-year rate 33.4%. 14 Stage I II 46.4%. 18 III IV 20.7%. For 42 dissection adjacent...