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...

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...

Evolutionary information on species divergence times is fundamental to studies of biodiversity, development, and disease. Molecular dating has enhanced our understanding the temporal patterns divergences over last five decades, number increasing quickly due an exponential growth in available collection molecular sequences from diverse large genes. Our TimeTree resource a public knowledge-base with primary focus make all derived using sequence data scientists, educators, general consistent...

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...

Abstract Summary: Biologists and other scientists routinely need to know times of divergence between species construct phylogenies calibrated time (timetrees). Published studies reporting estimates from molecular data have been increasing rapidly, but the largely inaccessible greater community because their complexity. TimeTree brings these together in a consistent format uses hierarchical structure, corresponding tree life, maximize utility. Results are presented summarized, allowing users...

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...

Genomic data are rapidly resolving the tree of living species calibrated to time, timetree life, which will provide a framework for research in diverse fields science. Previous analyses taxonomically restricted timetrees have found decline rate diversification many groups organisms, often attributed ecological interactions among species. Here, we synthesized global life from 2,274 studies representing 50,632 and examined pattern as well timing speciation. We that diversity has been mostly...

Abstract We present the fifth edition of TimeTree Life resource (TToL5), a product timetree life project that aims to synthesize published molecular timetrees and make evolutionary knowledge easily accessible all. Using TToL5 web portal, users can retrieve studies divergence times between species, timeline species’ evolution beginning with origin life, for given group at desired taxonomic rank. contains time information on 137,306 41% more than previous edition. The interface is now...

Abstract A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given phylogeny and extant species. model substitution employed to analyze data present-day sequences, maximum likelihood estimates parameters such as branch lengths were used compare posterior probabilities assignments character states (nucleotides acids) interior nodes tree; assignment having highest probability best reconstruction at site. The lysozyme c six mammals...

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...

Knowledge of the rate point mutation is fundamental importance, because mutations are a vital source genetic novelty and significant cause human diseases. Currently, thought to vary many fold among genes within genome lineages in mammals. We have conducted computational analysis 5,669 (17,208 sequences) from species representing major groups placental mammals characterize extent differences diverse mammalian lineages. find that approximately constant per year largely similar genes....

In the past, molecular clocks have been used to estimate divergence times among animal phyla, but those time estimates varied widely (1200–670 million years ago, Ma). order obtain that are more robust, we analysed a larger number of genes for divergences three well–represented and plants, animals fungi. The chordate–arthropod divergence, using 50 genes, is 993 ± 46 Ma. Nematodes were found diverged from lineage leading arthropods chordates at 1177 79 Phylogenetic analyses also show basal...

Abstract Phylogenetic trees from multiple genes can be obtained in two fundamentally different ways. In one, gene sequences are concatenated into a super‐gene alignment, which is then analyzed to generate the species tree. other, phylogenies inferred separately each gene, and consensus of these used represent Here, we have compared approaches by means computer simulation, using 448 parameter sets, including evolutionary rate, sequence length, base composition, transition/transversion rate...