MEGA2: molecular evolutionary genetics analysis software

By Sudhir Kumar, Koichiro Tamura, Ingrid B. Jakobsen, Masatoshi Nei. Bioinform., 2001

6,309 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/725a3cbac5e12ee0dcd1dbd036929dc6d7783b58

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Citations in the corpus

Timing of the population dynamics of bullhead Cottus gobio (Teleostei: Cottidae) during the Pleistocene (2002, neutral): “(Strimmer & von Haeseler, 1996) and MEGA vs. 2.1 (Kumar et al., 2001).”
Alkylation damage in DNA and RNA--repair mechanisms and medical significance. (2004, methodology): “The phylogeny was computed in Mega2[166] with the Minimum Evolution algorithm using the Poisson correction for amino acid distances, complete deletion of gap sites, and a Close-Neighbour-Interchange search starting from the Neighbour-Joining tree.”
Mitochondrial differentiation and biogeography of Hyla meridionalis (Anura: Hylidae): an unusual phylogeographical pattern (2007, methodology): “Mean sequence divergence between groups was calculated with mega2 (Kumar et al., 2001).”
Evolutionary distance estimation under heterogeneous substitution pattern among lineages. (2002, methodology): “These methods will be made available in the computer software MEGA2 (Kumar et al. 2001) available from http://www.megasoftware.net.”
Complete Genomic Sequence of Human Coronavirus OC43: Molecular Clock Analysis Suggests a Relatively Recent Zoonotic Coronavirus Transmission Event (2005, methodology): “Phylogenetic analyses were conducted by using MEGA, version 2.1 ( 34 ).”
The alternation of different morphotypes in the seasonal cycle of the toxic diatom Pseudo-nitzschia galaxiae (2005, methodology): “1 computer package (Kumar et al., 2001); the maximum parsimony trees were performed using the parsimony option in MEGA 2.”
CHARACTERIZATION OF OSTREOPSIS AND COOLIA (DINOPHYCEAE) ISOLATES IN THE WESTERN MEDITERRANEAN SEA BASED ON MORPHOLOGY, TOXICITY AND INTERNAL TRANSCRIBED SPACER 5.8S rDNA SEQUENCES 1 (2005, methodology): “The mean pair-wise nucleotide difference number (Nei 1987) for the entire 5.8S rDNA and ITS region sequences within and among C. monotis and Ostreopsis spp. isolates was calculated with MEGA, version 2.0 (Kumar et al. 2001).”
From Europe to Africa and vice versa: evidence for multiple intercontinental dispersal in ribbed salamanders (Genus Pleurodeles) (2004, methodology): “We used the MEGA software, version 2.1 (Kumar et al., 2001), to estimate times of divergence of splits; 95% confidence limits of estimates of divergence time were calculated via 1000 bootstrap replicates.”
MHC Variability of a Small Lemur in the Littoral Forest Fragments of Southeastern Madagascar (2004, methodology): “MEGA (Kumar et al. 2001) was used to construct the neighbour-joining tree using the genetic distances of Jukes and Cantor (1969) and to calculate the relative rate of non-synonymous and synonymous substitutions according to Nei and Gojobori (1986), applying the correction of Jukes and Cantor (1969) ”
Regulation of vitellogenin genes in insects (2014, methodology): “A distance analysis of amino acid sequences was performed using CLUSTAL W software and used as input for a neighbor-joining tree construction program MEGA3 (Kumar et al. 2001).”
Inference of Bacterial Microevolution Using Multilocus Sequence Data (2007, methodology): “The genealogies were drawn using the radial tree option of Mega ( Kumar et al., 2001 ) and share a common scale.”
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment (2004, methodology): “…26 Yes Yes (G+C) Yes Yes Tajima–Nei 27 Yes Yes Yes Tamura–Nei 25 Yes Yes Yes Yes Log-Det For computing synonymous and non-synonymous distances, both the Nei– Gojobori 34 and Li–Wu–Luo 35 methods and their modiﬁcations, 9,36–40 which account for transition/transversion bias, are available in MEGA.”