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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Bacteriophage Combinations Significantly Reduce Clostridium difficile Growth In Vitro and Proliferation In Vivo
Janet Y. Nale,Janice Spencer,Katherine R. Hargreaves,Anthony M. Buckley,Przemysław Trzepiński,Gillian Douce,Martha R. J. Clokie +6 more
TL;DR: Detailed host range analysis of six myoviruses and one siphovirus was conducted on 80 strains representing 21 major epidemic and clinically severe ribotypes, demonstrating the therapeutic potential of phage combinations to treat CDI.
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In silico prediction of potential inhibitors for the main protease of SARS-CoV-2 using molecular docking and dynamics simulation based drug-repurposing.
TL;DR: Among the library of FDA approved antiviral drugs, the top three inhibitors Lopinavir-Ritonavir, Tipranavir and Raltegravir show the best molecular interaction with the main protease of SARS-CoV-2.
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SymPortal: A novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling.
Benjamin C. C. Hume,Edward G. Smith,Maren Ziegler,Hugh J. M. Warrington,John A. Burt,Todd C. LaJeunesse,Joerg Wiedenmann,Christian R. Voolstra +7 more
TL;DR: It is considered that SymPortal, in conjunction with ongoing large‐scale sampling and sequencing efforts, should play an instrumental role in making future sampling efforts more comparable and in maximizing their efficacy in working towards the classification of the global Symbiodiniaceae diversity.
Journal ArticleDOI
The Genome of Artemisia annua Provides Insight into the Evolution of Asteraceae Family and Artemisinin Biosynthesis.
Qian Shen,Lida Zhang,Zhihua Liao,Shengyue Wang,Tingxiang Yan,Shi Pu,Meng Liu,Xueqing Fu,Qifang Pan,Yuliang Wang,Zongyou Lv,Xu Lu,Xu Lu,Fangyuan Zhang,Fangyuan Zhang,Weimin Jiang,Yanan Ma,Minghui Chen,Xiaolong Hao,Ling Li,Yueli Tang,Gang Lv,Yan Zhou,Xiaofen Sun,Peter E. Brodelius,Jocelyn K. C. Rose,Kexuan Tang +26 more
TL;DR: A high-quality draft assembly is reported of the 1.74-gigabase genome of A. annua, which is highly heterozygous, rich in repetitive sequences, and contains 63 226 protein-coding genes, one of the largest numbers among the sequenced plant species.
Journal ArticleDOI
Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity
Renmao Tian,Daliang Ning,Zhili He,Ping Zhang,Sarah J. Spencer,Shu-Hong Gao,Weiling Shi,Linwei Wu,Ya Zhang,Yunfeng Yang,Benjamin G. Adams,Andrea M. Rocha,Brittny L. Detienne,Kenneth A. Lowe,Dominique C. Joyner,Dawn M. Klingeman,Adam P. Arkin,Adam P. Arkin,Matthew W. Fields,Terry C. Hazen,Terry C. Hazen,David A. Stahl,Eric J. Alm,Jizhong Zhou,Jizhong Zhou,Jizhong Zhou +25 more
TL;DR: It is found that Patescibacteria has streamlined many functions while acquiring advantages such as avoiding phage invasion, to adapt to the groundwater environment, and demonstrates a case where less is more, and small is mighty.
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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