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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Identification and distribution of the NBS-LRR gene family in the Cassava genome
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Extracellular synthesis of silver nanoparticles by Pseudomonas sp. THG-LS1.4 and their antimicrobial application.
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Journal ArticleDOI
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference
Lasse Maretty,Jacob Malte Jensen,Bent O. Petersen,Jonas Andreas Sibbesen,Siyang Liu,Palle Villesen,Laurits Skov,Kirstine Belling,Christian Theil Have,Jose M. G. Izarzugaza,Marie Grosjean,Jette Bork-Jensen,Jakob Grove,Jakob Grove,Thomas Damm Als,Thomas Damm Als,Shujia Huang,Yuqi Chang,Ruiqi Xu,Weijian Ye,J. S. Rao,Xiaosen Guo,Jihua Sun,Hongzhi Cao,Chen Ye,Johan van Beusekom,Thomas Espeseth,Thomas Espeseth,Esben N. Flindt,Rune Møllegaard Friborg,Anders E. Halager,Stephanie Le Hellard,Stephanie Le Hellard,Christina M. Hultman,Francesco Lescai,Francesco Lescai,Shengting Li,Shengting Li,Ole Lund,Peter Løngren,Thomas Mailund,Maria Luisa Matey-Hernandez,Ole Mors,Ole Mors,Christian N. S. Pedersen,Thomas Sicheritz-Pontén,Patrick F. Sullivan,Patrick F. Sullivan,Ali Syed,David Westergaard,Rachita Yadav,Ning Li,Xun Xu,Torben Hansen,Anders Krogh,Lars Bolund,Thorkild I. A. Sørensen,Thorkild I. A. Sørensen,Oluf Pedersen,Ramneek Gupta,Simon Rasmussen,Søren Besenbacher,Anders D. Børglum,Anders D. Børglum,Jun Wang,Jun Wang,Hans Eiberg,Karsten Kristiansen,Søren Brunak,Søren Brunak,Mikkel H. Schierup +70 more
TL;DR: This study provides a regional reference genome that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases and is expected to improve the power of future association mapping studies and pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.
References
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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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