Journal ArticleDOI
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.Abstract:
Summary: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. Availability: http://www.megasoftware.net.read more
Citations
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Genetic Composition of Human Immunodeficiency Virus Type 1 in Cerebrospinal Fluid and Blood without Treatment and during Failing Antiretroviral Therapy
Matthew C. Strain,S. Letendre,Satish K. Pillai,T. Russell,Caroline Ignacio,Huldrych F. Günthard,Benjamin M. Good,Darren M. Smith,Steven M. Wolinsky,Manohar R. Furtado,Jennifer Marquie-Beck,Janis Durelle,Igor Grant,Douglas D. Richman,Douglas D. Richman,Thomas D. Marcotte,McCutchan Ja,Ronald J. Ellis,Joseph K. Wong,Joseph K. Wong +19 more
TL;DR: The study of CSF HIV as an accessible surrogate for HIV virions in the brain is supported, the high frequency of discordant resistance in subjects with advanced disease in the absence of opportunistic infection or malignancy of the CNS is confirmed, and genetic patterns in HIV env associated with adaptation to the CNS are identified.
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The molecular epidemiology of dengue virus serotype 4 in Bangkok, Thailand.
TL;DR: A large-scale molecular epidemiological analysis of Dengue virus serotype 4 (DENV-4) in Thailand was conducted by as mentioned in this paper, which revealed extensive genetic diversity within a single locality at a single time and a pattern of continual lineage turnover.
Journal ArticleDOI
A genomewide survey of developmentally relevant genes in Ciona intestinalis. I. Genes for bHLH transcription factors.
TL;DR: The present analysis provides an insight into the basic set of bHLH genes that the last common ancestor of ascidian and vertebrates had, and will provide important background information for future studies using ascidians as a model system for vertebrate development.
Journal ArticleDOI
An α2-macroglobulin-like protein is the cue to gregarious settlement of the barnacle Balanus amphitrite
Catherine Dreanno,Kiyotaka Matsumura,Naoshi Dohmae,Koji Takio,Hiroshi Hirota,Richard R. Kirby,Anthony S. Clare +6 more
TL;DR: It is reported that a biological cue to gregarious settlement, the settlement-inducing protein complex (SIPC), of the major fouling barnacle Balanus amphitrite is a previously undescribed glycoprotein that may have evolved by duplication from an ancestral α2-macroglobulin gene.
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Proposal to create subspecies of Rickettsia conorii based on multi-locus sequence typing and an emended description of Rickettsia conorii.
TL;DR: Although homogeneous genotypically, strains within the R. conorii species show MST genotypes, serotypic, and epidemio-clinical dissimilarities, and it is proposed to modify the nomenclature of the rickettsiae through the creation of subspecies.
References
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Book
Molecular Evolution and Phylogenetics
Masatoshi Nei,Sudhir Kumar +1 more
TL;DR: This chapter discusses the molecular basis of evolution, the evolution of organisms based on the fossil record, and the implications of these events for phylogenetic inference.
Journal ArticleDOI
MEGA: Molecular Evolutionary Genetics Analysis software for microcomputers
TL;DR: 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.
Book
Molecular Evolution: A Phylogenetic Approach
TL;DR: The Archaeology of the Genome Trees Genes: Organization, Function and Evolution Genes in Populations Measuring Genetic Change Inferring Molecular Phylogeny Models of Molecular Evolution Applications of molecular phylogenetics as mentioned in this paper.
Journal ArticleDOI
Phylogenetic test of the molecular clock and linearized trees.
TL;DR: To estimate approximate divergence times of species or species groups with molecular data, a method of constructing a linearized tree under the assumption of a molecular clock is developed and used to analyze hominoid mitochondrial DNA and drosophilid Adh gene sequences.
Journal ArticleDOI
Molecular Evolution — A Phylogenetic Approach.
TL;DR: The authors set themselves the tasks of showing how evolutionary information is written into gene sequences and describing the methods by which such information can be recovered and succeed, providing a wealth of examples and setting many of them in a historical perspective.
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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
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