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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Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project
Roger Horton,Richard Gibson,Penny Coggill,Marcos Mateo Miretti,Richard J.N. Allcock,J P Almeida,Simon A. Forbes,James G. R. Gilbert,Karen Halls,Jennifer Harrow,E. Hart,Kevin L. Howe,David K. Jackson,Sophie Palmer,Anne N. Roberts,Sarah Sims,C. Andrew Stewart,James A. Traherne,Steve Trevanion,Laurens G. Wilming,Jane Rogers,Pieter J. de Jong,John F. Elliott,Stephen Sawcer,John A. Todd,John Trowsdale,Stephan Beck,Stephan Beck +27 more
TL;DR: The MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHChaplotype in the European population.
Journal ArticleDOI
Swine and Poultry Pathogens: the Complete Genome Sequences of Two Strains of Mycoplasma hyopneumoniae and a Strain of Mycoplasma synoviae
Ana Tereza Ribeiro de Vasconcelos,Henrique Bunselmeyer Ferreira,Cristiano Valim Bizarro,Sandro L. Bonatto,Marcos Oliveira de Carvalho,Paulo Marcos Pinto,Darcy F. de Almeida,Luiz Gonzaga Paula de Almeida,Almeida Rosana De,Leonardo Alves-Filho,Enedina Nogueira de Assunção,Vasco Azevedo,Maurício Reis Bogo,Marcelo M. Brigido,Marcelo Brocchi,Marcelo Brocchi,Hélio Almeida Burity,Anamaria A. Camargo,Sandro da Silva Camargo,Marta S. P. Carepo,Dirce Maria Carraro,J.C.M. Cascardo,Luiza Amaral de Castro,Gisele Cavalcanti,Gustavo Chemale,Rosane G. Collevatti,Cristina W. Cunha,Bruno Dallagiovanna,Bibiana Paula Dambrós,Odir Antônio Dellagostin,Clarissa Falcão,Fabiana Fantinatti-Garboggini,Maria Sueli Soares Felipe,Laurimar Fiorentin,Glória Regina Franco,Nara Suzy Aguiar De Freitas,Diego Frias,Thalles B. Grangeiro,Edmundo C. Grisard,Claudia Teixeira Guimarães,Mariangela Hungria,Silvia Neto Jardim,Marco Aurélio Krieger,Jomar Pereira Laurino,Lucymara Fassarella Agnez Lima,Maryellen I. Lopes,Élgion Lúcio da Silva Loreto,Humberto Maciel França Madeira,Gilson P. Manfio,Andrea Queiroz Maranhão,Christyanne T. Martinkovics,Silvia Regina Batistuzzo de Medeiros,Miguel Angêlo Martins Moreira,Márcia Neiva,Cicero Eduardo Ramalho-Neto,Marisa Fabiana Nicolás,Sergio C. Oliveira,Roger Ferreira Cury Paixão,Fábio O. Pedrosa,Sérgio D.J. Pena,Maristela Pereira,Lilian Pereira-Ferrari,Itamar Antônio Piffer,Luciano da Silva Pinto,Deise Porto Potrich,Anna Christina M. Salim,Fabrício R. Santos,Renata Schmitt,Maria Paula Cruz Schneider,Augusto Schrank,Irene Silveira Schrank,Adriana F. Schuck,Héctor N. Seuánez,Denise Wanderlei Silva,Rosane Silva,Sergio Ceroni da Silva,Célia Maria de Almeida Soares,Kelly Rose Lobo de Souza,Rangel C. Souza,Charley Christian Staats,Maria B. R. Steffens,Santuza M. R. Teixeira,Turán P. Ürményi,Marilene Henning Vainstein,Luciana W. Zuccherato,Andrew J. G. Simpson,Arnaldo Zaha +86 more
TL;DR: Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species, and indicated a likely transfer event of hemagglutinin-coding DNA sequences from M. gallisepticum to M. synoviae.
Journal ArticleDOI
Fuzzy species among recombinogenic bacteria
TL;DR: A multilocus approach using large samples of closely related isolates delineates species even in the highly recombinogenic human Neisseria where individual loci are inadequate for the task.
Journal ArticleDOI
Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level
TL;DR: Phylogenetic analyses based on 16S rDNA sequences revealed that both strains belong to an uncultured, previously recognized clone lineage of the phylum Chloroflexi (formerly known as green non-sulfur bacteria) and suggested that each strain should be classified into a new independent genus.
Journal ArticleDOI
Proteiniphilum acetatigenes gen. nov., sp. nov., from a UASB reactor treating brewery wastewater.
Shuangya Chen,Xiuzhu Dong +1 more
TL;DR: A new genus and species, Proteiniphilum acetatigenes gen. nov., is proposed, with strain TB107T (=JCM 12891T=AS 1.5024T) as the type strain, with <91 % 16S rRNA gene sequence similarity to the closest species with validly published names.
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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