Prospects for inferring very large phylogenies by using the neighbor-joining method.

By Koichiro Tamura, Masatoshi Nei, Sudhir Kumar. Proceedings of the National Academy of Sciences of the United States of America, 2004

5,576 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/6f604b37408da4fddcb15f56af376c672be87da8

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Citations in the corpus

Microbial degradation of imidacloprid and toxicological analysis of its biodegradation metabolites in silkworm (Bombyx mori) (2013, methodology): “The evolutionary distances were computed using the Maximum Composite Likelihood method [20] and were in the units of the number of base substitutions per site.”
Correlation between microbial community structure and biofouling in a laboratory scale membrane bioreactor with synthetic wastewater (2012, methodology): “Evolutionary distance matrices were generated according to the maximum composite likelihood method [23].”
Endophytic fungi harbored in Cannabis sativa L.: diversity and potential as biocontrol agents against host plant-specific phytopathogens (2013, methodology): “The evolutionary distances were computed using the Maximum Composite Likelihood method (Tamura et al. 2004) and were calculated in the units of the number of base substitutions per site.”
DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution (2013, background): “These SE distances alleviated or eliminated the three major problems associated with the independently estimated distances (Tamura et al. 2004; Xia 2009) and reduced the documented topological biases associated with the over- and underestimated distances (Xia 2006).”
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. (2011, methodology): “…or generated automatically by applying NJ and BIONJ algorithms to a matrix of pairwise distances estimated using a maximum composite likelihood approach for nucleotide sequences and a JTT model for amino acid sequences (Saitou and Nei 1987; Jones et al. 1992; Gascuel 1997; Tamura et al. 2004).”
MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. (2007, methodology): “This approach was previously referred to as the ‘‘Simultaneous Estimation’’ (SE) method, because all dij’s are simultaneously estimated (Tamura, Nei, and Kumar 2004).”
Phylogenic diversity of fungal endophytes in Spanish stands of Pinus halepensis (2011, neutral): “The evolutionary distances were computed using the Maximum Composite Likelihood method (Tamura et al. 2004) and are in the units of the number of base substitutions per site.”
Comparative Genomics in Eukaryotes (2005, background): “In support of such large-scale phylogenetic efforts, it has recently been shown that current methods for constructing phylogenetic trees can be scaled up to infer very large phylogenies (Tamura et al., 2004).”
Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV (2020, methodology): “The evolutionary distances were calculated using the Maximum Composite Likelihood method [18].”