MEGA11: Molecular Evolutionary Genetics Analysis Version 11

@article{Tamura2021MEGA11ME,
  title={MEGA11: Molecular Evolutionary Genetics Analysis Version 11},
  author={Koichiro Tamura and Glen Stecher and Sudhir Kumar},
  journal={Molecular Biology and Evolution},
  year={2021},
  volume={38},
  pages={3022 - 3027}
}
Abstract The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating… 

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References

SHOWING 1-10 OF 24 REFERENCES
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
TLDR
An advanced version of the Molecular Evolutionary Genetics Analysis software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis, is released, which enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny.
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.
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.
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
TLDR
An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets.
TLDR
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.
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.
A new method for inferring timetrees from temporally sampled molecular sequences
TLDR
A new method for inferring timetrees for phylogenies with tip dates is developed, which improves on widely-used Bayesian methods and does not require prior specification of population parameters, branch rate model, or clock model.
MEGA2: molecular evolutionary genetics analysis software
TLDR
MEGA2 vastly extends the capabilities of MEGA version 1 by facilitating analyses of large datasets, enabling creation and analyses of groups of sequences, and expanding the repertoire of statistical methods for molecular evolutionary studies.
A Molecular Evolutionary Reference for the Human Variome.
TLDR
A new molecular evolutionary method for estimating neutral evolutionary probabilities (EPs) of each amino acid, or nucleotide state at a genomic position without using intraspecific polymorphism data, found that EPs accurately predict neutral and disease-associated alleles.
...
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