MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.

  title={MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.},
  author={Koichiro Tamura and Glen Stecher and Daniel Peterson and Alan J. Filipski and Sudhir Kumar},
  journal={Molecular biology and evolution},
  volume={30 12},
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. [...] Key Method This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied…Expand
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
The latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine, has been optimized for use on 64-bit computing systems for analyzing larger datasets.
MEGA11: Molecular Evolutionary Genetics Analysis Version 11
New additions are described that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods and a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments.
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Critical assessment of phylogenetic algorithms
Phylogenetic analyses are important part of the biological research, the idea behind which is that species are related through a history of common descent. A main goal of phylogenetics is to
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The statistical models and algorithms used to reconstruct phylogenetic trees are introduced, advances in the exploration and utilization of plant genomes for molecular phylogenetic analyses are discussed, and molecular data provide a large number of datapoints and enable comparisons from diverse taxa.
Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization.
This work reproduces key findings from recent comparative genomics studies, including a reanalysis of the EGLN1 gene from the tiger genome study, and demonstrates a typical workflow using Wasabi.
SWPhylo – A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees
  • Xiaoyu Yu, O. Reva
  • Computer Science, Medicine
    Evolutionary bioinformatics online
  • 2018
It is demonstrated that the annotation- and alignment-free comparison of genome-wide tetranucleotide frequencies, termed oligonucleotide usage patterns (OUPs), allowed a fast and reliable inference of phylogenetic trees.
Molecular Footprint of Kenya’s Gene Bank Repositories Based on the cp -Genome Signatures
An extensive study on characterizing the genetic diversity of cp-DNA gene sequence data for the cowpea accessions from the Nation Gene Bank of Kenya, and examines the efficacy of custom DNA barcode loci for identification success and compared phylogenetic diversity measures between sites and among variants.
Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals
It is shown that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ.


MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis
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
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.
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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
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
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
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
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
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)]