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.Abstract:
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 inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. 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. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.read more
Citations
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Molecular Epidemiology of
Laguna Negra,Elizabeth Salbé Travassos da Rosa,Darlene B. Simith,Sharlene L Pereira,Mauro R. Elkhoury,Elizabeth Davi Santos,Marília Lavocat,Aparecido A. R. Marques,Vânia A. Kohl,Cibele R. Bonvicino,Elba Regina Sampaio de Lemos +10 more
Journal ArticleDOI
S1 gene-based phylogeny of infectious bronchitis virus: An attempt to harmonize virus classification.
Viviana Valastro,Edward C. Holmes,Paul Britton,Alice Fusaro,Mark W. Jackwood,Giovanni Cattoli,Isabella Monne +6 more
TL;DR: It is suggested that the inference of phylogenetic relationships alone represents a more appropriate criterion for sequence classification than pairwise sequence comparisons and is crucial for future studies of IBV epidemiology and evolution.
Journal ArticleDOI
Zika virus: a previously slow pandemic spreads rapidly through the Americas.
Derek Gatherer,Alain Kohl +1 more
TL;DR: Its clinical profile is that of a dengue-like febrile illness, but associations with Guillain-Barré syndrome and microcephaly have appeared recently.
Journal ArticleDOI
Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic.
Rebeca Martín,Sylvie Miquel,Sylvie Miquel,Leandro de Jesus Benevides,Leandro de Jesus Benevides,Chantal Bridonneau,Véronique Robert,Sylvie Hudault,Florian Chain,Olivier Berteau,Vasco Azevedo,Jean M. Chatel,Harry Sokol,Harry Sokol,Luis G. Bermúdez-Humarán,Muriel Thomas,Philippe Langella +16 more
TL;DR: The results suggest that some F. prausnitzii strains could represent good candidates as next-generation probiotic as well as a deep molecular and metabolic characterization of these isolated strains.
The Genome of Chenopodium quinoa
TL;DR: In this article, the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome contact and genetic maps, was reported.
References
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Journal ArticleDOI
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: 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.
Journal ArticleDOI
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Book
The Neutral Theory of Molecular Evolution
TL;DR: The neutral theory as discussed by the authors states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
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