MEGA (Molecular Evolutionary Genetics Analysis)

By Michael P. Cummings. 2004

2,278 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/662d765bb8ce832c6f6f65c495c29af3a204d03a

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In Genetics

In Molecular Biology

Citations in the corpus

Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae) (2005, methodology): “MEGA (Kumar et al., 2001) was used to calculate p-distances (Nei, 1987) and standard errors within and among taxa.”
Genetic divergence, phylogeography and conservation units of giant tortoises from Santa Cruz and Pinzón, Galápagos Islands (2004, methodology): “This approach is indicated for analyses of the mtDNA control region and for data sets with different rates of transitions and transversions (Kumar et al. 1993).”
Chapter 10 Metabolic and Molecular Responses of Fish to Hypoxia (2009, methodology): “Sequences were aligned using ClustalW and phylogenetic analysis was performed using the neighbor-joining methods with complete deletion of gaps using MEGA2 software (Kumar et al., 2001).”
Intraspecific genetic diversity of the endemic freshwater crab Candidiopotamon rathbunae (Decapoda, Brachyura, Potamidae) reflects five million years of the geological history of Taiwan (2006, methodology): “The ME tree was constructed with the program MEGA2 (version 2.1, Kumar et al., 2001) with the gamma correction obtained from MODELTEST, the Kimura (1980) two-parameter model, and 2000 bootstrap reiterations (CNI level ¼ 2, initial tree ¼ NJ, and max. number of trees to retain ¼ 1).”
An enhanced MITOMAP with a global mtDNA mutational phylogeny (2006, methodology): “The core topology of the tree was generated by the neighbor-joining program from MEGA (28) using 1060 human mtDNA sequences.”
From Europe to Africa and vice versa: evidence for multiple intercontinental dispersal in ribbed salamanders (Genus Pleurodeles) (2004, methodology): “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.”
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo (2016, methodology): “The alignment length ranged from 658 bp to 1620 bp, while the proportion of variable nucleotides, measured by the P-Distance (MEGA v5.2; Tamura et al., 2011) averaged over the sequences of each dataset , varied from 2.”
Phylogenetic Relationships of Spider Monkeys (Ateles) Based on Mitochondrial DNA Variation (2000, methodology): “We also used the computer phylogeny program MEGA Vs 1.02 (Kumar et al., 1993) to compute the standard error test of neighbor-joining tree branch lengths from zero H0:BL 0.”
Phylogenetic analysis and a time tree for a large drosophilid data set (Diptera: Drosophilidae) (2013, methodology): “Alignments were conducted separately for each nuclear marker using CLUSTALW with amino-acid translation performed using the MEGA 4 platform (Tamura et al., 2007).”
Analysis of genetic diversity among different geographical populations and determination of biotypes of Bemisia tabaci in China (2005, methodology): “Phylogenetic trees were constructed using molecular evolutionary genetics analysis (version 2.1, MEGA 2) software (Kumar et al., 2001) based on the unweighted pair-group method of the arithmetic average (UPGMA).”
New insights into the phylogeny, systematics and DNA barcoding of Nemertea (2014, methodology): “5 (Tamura et al. 2011) was used to calculate intraspecific variations and interspecific divergences among the samples using the following settings: uncorrected p-distances, uniform rates among sites and pairwise deletion of gaps for first, second and third codon positions.”
Productivity and diversity of morel mushrooms in healthy, burned, and insect-damaged forests of northeastern Oregon (2004, methodology): “The p distance setting was used to derive the distance matrix (Puterka et al., 1993; Kumar et al., 2000).”