• Corpus ID: 51553929

Evolutionary Genetics Analysis Version 6 . 0

@inproceedings{Tamura2013EvolutionaryGA,
  title={Evolutionary Genetics Analysis Version 6 . 0},
  author={Koichiro Tamura and Glen Stecher and Daniel Peterson and Alan J. Filipski and Sudhir Kumar},
  year={2013}
}
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree… 

Figures from this paper

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web
TLDR
Phylo.io is introduced, a web application to visualize and compare phylogenetic trees side-by-side and has distinctive features are: highlighting of similarities and differences between two trees, automatic identification of the best matching rooting and leaf order, scalability to large trees, high usability, multiplatform support via standard HTML5 implementation, and possibility to store and share visualizations.
The Timetree of Prokaryotes: New Insights into Their Evolution and Speciation.
TLDR
It is found that prokaryote diversification as a whole is the result of the random splitting of lineages and is neither limited by existing diversity (filled niches) nor responsive in any major way to environmental changes.
gmos: Rapid Detection of Genome Mosaicism over Short Evolutionary Distances
Prokaryotic and viral genomes are often altered by recombination and horizontal gene transfer. The existing methods for detecting recombination are primarily aimed at viral genomes or sets of loci,
A novel molecular marker for the study of Neotropical cichlid phylogeny.
TLDR
The aim was to identify a new nuclear molecular marker that could establish the phylogeny of Neotropical cichlids and is potentially correlated with the visual system and Bayesian inference and maximum likelihood analysis were used to support the use of the nuclear opsin LWS gene.
TreeBASE a bioinformatics tool for phylogenetic analysis: Submission guidelines made easy
TLDR
The present communication would like to supplement the same and provide a simple, easy to perform TreeBASE submission guide.
The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies
TLDR
This study designed PCR primers to amplify 136 nuclear protein-coding loci by scanning the published Red Junglefowl and Zebra Finch genomes and showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci, indicating great potential to facilitate studies in avian phylogenetics and population genetics.
Multilocus phylogeny reconstruction: new insights into the evolutionary history of the genus Petunia.
TLDR
Based on nine nuclear and five plastid DNA markers, the phylogenetic analysis reinforces the monophyly of the genus Petunia and supports the hypothesis that the basal divergence is more related to the differentiation of corolla tube length, whereas the geographic distribution of species is morerelated to divergences within these main clades.
Genomic Profiles of Diversification and Genotype-Phenotype Association in Island Nematode Lineages.
TLDR
Taking a genome-wide association approach, this work functionally validate a significant genotype-phenotype association for pH tolerance in P. pacificus, which is undergoing heterogeneous genotypic and phenotypic diversification related to both evolutionary and environmental processes.
Evolutionary history and classification of Micropia retroelements in Drosophilidae species
TLDR
The evolutionary history of Micropia within Drosophilidae is assessed, including several VTTs and HTTs events, associated to ancestral polymorphisms and recurrentMicropia sequences diversification are proposed, and several cases of unexpected high levels of similarity are found in divergent species.
Genome evolution in a putatively asexual wasp
TLDR
It is hypothesized that the novel variation introduced by mutation along with limited shuffling of genes may facilitate initial adaptation and extend persistence of such lineages.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 11 REFERENCES
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis
TLDR
MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version, including methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference.
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers
TLDR
In this program, various methods for estimating evolutionary distances from nucleotide and amino acid sequence data, three different methods of phylogenetic inference (UPGMA, neighbor-joining and maximum parsimony) and two statistical tests of topological differences are included.
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.
TLDR
The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small.
  • M. Nei, S. Kumar, K. Takahashi
  • Mathematics, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
This finding indicates that the optimization principle tends to give incorrect topologies when n is small, and it is suggested that more attention should be given to testing the statistical reliability of an estimated tree rather than to finding the optimal tree with excessive efforts.
Molecular Evolution and Phylogenetics
TLDR
This chapter discusses the molecular basis of evolution, the evolution of organisms based on the fossil record, and the implications of these events for phylogenetic inference.
Estimating divergence times in large molecular phylogenies
TLDR
RelTime is presented, a method that estimates relative times of divergences for all branching points (nodes) in very large phylogenetic trees without assuming a specific model for lineage rate variation or specifying any clock calibrations.
TimeTree2: species divergence times on the iPhone
TLDR
TimeTree2 is a public knowledgebase that enables data-driven access to the collection of peer-reviewed publications in molecular evolution and phylogenetics that have reported estimates of time of divergence between species.
Estimating the Rate of Intersubtype Recombination in Early HIV-1 Group M Strains
TLDR
The results imply that intersubtype recombination may have occurred in approximately 20% of lineages evolving over a period of 30 years and confirm intersub type recombination as a substantial force in generating HIV-1 group M diversity.
MEGA 5 : molecular evolutionary genetics analysis using maximum likelihood , evolutionary distance , and maximum parsimony meth
  • Mol Biol Evol .
  • 2011
PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)]
...
1
2
...