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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In silico Prediction, Characterization, Molecular Docking, and Dynamic Studies on Fungal SDRs as Novel Targets for Searching Potential Fungicides Against Fusarium Wilt in Tomato.
Mohd Aamir,Vinay Kumar Singh,Manish Kumar Dubey,Mukesh Meena,Mukesh Meena,Sarvesh Pratap Kashyap,Sudheer Kumar Katari,Ram Sanmukh Upadhyay,Amineni Umamaheswari,Surendra Singh +9 more
TL;DR: It is concluded that the FOXG_04696, could be employed as a novel candidate protein, for structure-based design, and screening of target fungicides against the FOL pathogen.
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Burkholderia humptydooensis sp. nov., a New Species Related to Burkholderia thailandensis and the Fifth Member of the Burkholderia pseudomallei Complex.
Apichai Tuanyok,Mark Mayo,Holger C. Scholz,Carina M. Hall,Christopher J. Allender,Mirjam Kaestli,Jennifer L. Ginther,Senanu Spring-Pearson,Molly C. Bollig,Joshua K. Stone,Erik W. Settles,Joseph D. Busch,Lindsay C. Sidak-Loftis,Jason W. Sahl,Astrid Thomas,Lisa Kreutzer,Enrico Georgi,Jay E. Gee,Richard A. Bowen,Jason T. Ladner,Sean Lovett,G. I. Koroleva,Gustavo Palacios,David M. Wagner,Bart J. Currie,Paul Keim +25 more
TL;DR: Molecular analyses clearly demonstrated that strains MSMB43T, MSMB121, and MSMB122 belong to a novel Burkholderia species for which the name Burk holderia humptydooensis sp.
Journal ArticleDOI
Evolutionary Analyses of GRAS Transcription Factors in Angiosperms.
TL;DR: This study establishes a consistent framework for the classification of GRAS members in angiosperm species, and thereby a tool to correctly establish the orthologous relationships ofGRAS genes in most of the food crops in order to facilitate any subsequent functional analyses in the GRAS gene family.
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The 3.2 Å Resolution Structure of a Receptor:CheA:CheW Signaling Complex Defines Overlapping Binding Sites and Key Residue Interactions within Bacterial Chemosensory Arrays
Xiaoxiao Li,Aaron D. Fleetwood,Camille Bayas,Alexandrine M. Bilwes,Davi R. Ortega,Joseph J. Falke,Igor B. Zhulin,Brian R. Crane +7 more
TL;DR: Despite the non-native receptor fold in the present crystal structure, the local helix-in-groove contacts of the crystallographic P5-receptor interaction are present in native arrays and are essential for receptor regulation of kinase activity.
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Identification, prevalence and pathogenicity of Colletotrichum species causing anthracnose of Capsicum annuum in Asia
Dilani D. de Silva,Johannes Z. Groenewald,Pedro W. Crous,Peter K. Ades,Andi Nasruddin,Orarat Mongkolporn,Paul J. Taylor +6 more
TL;DR: The existence of new, highly aggressive exotic species, such as C. javanense and C. scovillei, poses a biosecurity risk to production in countries which do not have adequate quarantine regulations to restrict the entry of exotic pathogens.
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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