MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

By Sudhir Kumar, Masatoshi Nei, Joel T. Dudley, Koichiro Tamura. Briefings Bioinform., 2008

3,562 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/6c4705433d923a9abb37ff25708ab0253d94c5b4

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Citations in the corpus

From Mediterranean shores to central Saharan mountains: key phylogeographical insights from the genus Myrtus (2012, methodology): “New sequences were checked, edited, and assembled using mega4 (Kumar et al., 2008) and submitted to GenBank (Appendix S3).”
A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library. (2014, positive): “The sequencing data were aligned using MEGA5 software [26] against the wild-type (WT) CcdB sequence.”
Suppression of Magnaporthe oryzae by culture filtrates of Streptomyces globisporus JK-1 (2011, methodology): “0 software (Kumar et al., 2008) was used to carry out phylogenetic analyses of the alignment using the Neighbor-Joining method.”
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis (2012, neutral): “Summary: There is a growing need in the research community to apply the molecular evolutionary genetics analysis (MEGA) software tool for batch processing a large number of datasets and to integrate it into analysis workflows.”
Ribosomal Multi-Locus Sequence Typing: universal characterisation of bacteria from domain to strain (2012, methodology): “For larger datasets, up to the entire bacterial domain, the XMFA file was converted to an aligned concatenated sequence for 1006 Microbiology 158 neighbour-joining tree analysis using MEGA version 5 (Kumar et al., 2008), with ambiguous positions removed for each sequence pair.”
DNA barcoding in the red algal order Gelidiales: comparison of COI with rbc La nd verification of the "barcoding gap" (2010, methodology): “Sequences were aligned using MacClade (v. 4, Maddison & Maddison, 2000), and sequence divergences calculated and neighbor-joining trees and UPGMA cluster diagrams generated using PAUP* (v. 4.b10, Swofford, 2002) and MEGA (Kumar et al., 2008).”
Activity, abundance and community structure of anammox bacteria along depth profiles in three different paddy soils (2015, methodology): “The phylogenetic tree was constructed by using the neighbor-joining method in MEGA 5 software with 1000 bootstraps (Kumar et al., 2008).”
Abundance and community structure of ammonia-oxidizing bacteria and archaea in a temperate forest ecosystem under ten-years elevated CO2 (2012, methodology): “The Neighbor-joining method was followed to construct the phylogenetic tree using MEGA5 (Kumar et al., 2008) and based on the maximum composite likelihood model for calculating the evolutionary distance.”
Isolation of endophytic endospore-forming bacteria from Theobroma cacao as potential biological control agents of cacao diseases (2011, methodology): “0 (Kumar et al., 2008) to infer bacterial species.”
“Sight‐unseen” detection of rare aquatic species using environmental DNA (2011, methodology): “S. et al. (2010) A mark-recapture population estimate for invasive silver carp (Hypophthalmichthys molitrix) in the La Grange Reach, Illinois River. Biol Invasions 12, 433–436. Sampson, S.J., Chick J.H., Pegg M.A. (2009) Diet overlap among two Asian carp and three native fishes in backwater lakes on”
Persistence of Beauveria bassiana (Ascomycota: Hypocreales) as an endophyte following inoculation of radiata pine seed and seedlings (2012, methodology): “, 1990), then Beauveria sequences aligned with previously obtained sequences for the isolates F647 and F668 using DNAMan (Lynnon Biosoft, Canada) and MEGA (Kumar et al., 2008).”
Phylogenetic diversity of culturable fungi from the deep-sea sediments of the Central Indian Basin and their growth characteristics (2010, methodology): “Neighbour-joining (NJ) trees were created using pairwise genetic distances using MEGA 3.1 (Sudhir kumar et al. 2008).”