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
More filters
Journal ArticleDOI
Evolutionary and biomedical implications of a Schistosoma japonicum complementary DNA resource
Wei Hu,Qing Yan,Da-kang Shen,Feng Liu,Zhi-Dong Zhu,Huai-Dong Song,Xiangru Xu,Zhao-jun Wang,Yi-Ping Rong,Ling-Chun Zeng,Jian Wu,Xin Zhang,Ju-Jun Wang,Xue-Nian Xu,Shengyue Wang,Gang Fu,Xiang-Lin Zhang,Zhi-Qin Wang,Paul J. Brindley,Donald P. McManus,Chun-Liang Xue,Zheng Feng,Zhu Chen,Ze-Guang Han +23 more
TL;DR: S. japonicum encoded mammalian-like receptors for insulin, progesterone, cytokines and neuropeptides, suggesting that host hormones, or endogenous parasite homologs, could orchestrate schistosome development and maturation and thatSchistosomes modulate anti-parasite immune responses through inhibitors, molecular mimicry and other evasion strategies.
Journal ArticleDOI
Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce.
Sebastian Reyes-Chin-Wo,Zhiwen Wang,Xinhua Yang,Alexander Kozik,Siwaret Arikit,Chi Song,Liangfeng Xia,Lutz Froenicke,Dean Lavelle,Maria Jose Truco,Rui Xia,Shilin Zhu,Chunyan Xu,Huaqin Xu,Xun Xu,Kyle Cox,Ian F Korf,Blake C. Meyers,Blake C. Meyers,Richard W Michelmore +19 more
TL;DR: This work identifies several genomic features that may have contributed to the success of the Compositae family of flowering plants, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome.
Journal ArticleDOI
Amoebal Coculture of “Mycobacterium massiliense” sp. nov. from the Sputum of a Patient with Hemoptoic Pneumonia
Toïdi Adékambi,Martine Reynaud-Gaubert,Gilbert Greub,Gilbert Greub,Marie-José Gevaudan,Bernard La Scola,Didier Raoult,Michel Drancourt +7 more
TL;DR: Phenotypic and genotypic features of these two isolates indicated that they were representative of a new mycobacterial species within the M. chelonae-M.
Journal ArticleDOI
Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing
Toïdi Adékambi,Michel Drancourt +1 more
TL;DR: To assess further taxonomic relationships among RGM, complete sequences of the 16S rRNA gene, rpoB and recA and partial sequences of hsp65 and sodA were determined in 19 species of RGM and phylogenetic organizations obtained were globally similar to that inferred from combined datasets.
Journal ArticleDOI
Genome Sequence of an M3 Strain of Streptococcus pyogenes Reveals a Large-Scale Genomic Rearrangement in Invasive Strains and New Insights into Phage Evolution
Ichiro Nakagawa,Ken Kurokawa,Atsushi Yamashita,Masanobu Nakata,Yusuke Tomiyasu,Nobuo Okahashi,Shigetada Kawabata,Kiyoshi Yamazaki,Tadayoshi Shiba,Teruo Yasunaga,Hideo Hayashi,Masahira Hattori,Shigeyuki Hamada +12 more
TL;DR: Observations indicate that streptococcal phages represent important plasticity regions in the GAS chromosome where recombination between homologous phage genes can occur and result not only in new phage derivatives, but also in large chromosomal rearrangements.
References
More filters
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.
Related Papers (5)
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more