MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment

By Sudhir Kumar, Koichiro Tamura, Masatoshi Nei. Briefings Bioinform., 2004

12,311 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/80935b370bac09ce615a002caabc30fbb26f029b

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Citations in the corpus

Associating larvae and adults of Chinese Hydropsychidae caddisflies (Insecta:Trichoptera) using DNA sequences (2007, background): “1 (Kumar et al. 2004). the secondary structure (following Kjer 1995).”
A taxonomic reappraisal of the European Daphnia longispina complex (Crustacea, Cladocera, Anomopoda) (2008, neutral): “1 (Kumar et al. 2004).”
Concordant molecular and phenotypic data delineate new taxonomy and conservation priorities for the endangered mountain yellow‐legged frog (2007, methodology): “We used MEGA version 3.1 ( Kumar, Tamura & Nei, 2004 ) to calculate corrected pairwise mtDNA sequence divergence.”
Small but versatile: the extraordinary functional and structural diversity of the β-grasp fold (2007, methodology): “Additionally, trees were constructed using the neighbor-joining and minimum evolution methods as implemented in the MEGA program [132] and the Bayesian inference method using Markov chain Monte Carlo simulations implemented by the MRBAYES program [133].”
Detecting introgressive hybridisation in rock partridge populations (Alectoris graeca) in Greece through Bayesian admixture analyses of multilocus genotypes (2007, methodology): “A neighbour-joining tree (NJ; Saitou and Nei 1987), clustering pair wise Tamura-Nei’s (TN93; 1993) genetic distances between the aligned individual mtDNA CR haplotypes, was constructed using MEGA 3.0 (Kumar et al. 2004).”
Multiple introductions determine the genetic structure of an invasive species population: American mink Neovison vison in Poland (2010, methodology): “For visualization of the differences based on FST, dendrograms were constructed using the program Mega 4.1 (Kumar et al., 2004).”
Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome (2008, methodology): “Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment.”
Genealogical relationships within and among shallow-water Ciona species (Ascidiacea) (2007, methodology): “Sequences were edited and trimmed to 744 bp with SeqMan (DNASTAR) and aligned using the Clustal-W algorithm in MEGA 3.1 ( Kumar et al. 2004 ).”
Genome-Wide Comparative Analysis and Expression Pattern of TCP Gene Families in Arabidopsis thaliana and Oryza sativa (2007, positive): “0) software (http://www.megasoftware.net/index.html; Kumar et al. 2004) with the N-J method with the following parameters: Poisson correction, pairwise deletion, and bootstrap (1 000 replicates; random seed).”