The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Citations
63,427 citations
39,110 citations
Cites methods from "The neighbor-joining method: a new ..."
...MEGA5 automatically infers the evolutionary tree by the NeighborJoining (NJ) algorithm that uses a matrix of pairwise distances estimated under the Jones–Thornton–Taylor (JTT) model for amino acid sequences or the Tamura and Nei (1993) model for nucleotide sequences (Saitou and Nei 1987; Jones et al. 1992; Tamura and Nei 1993; Tamura et al. 2004)....
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...…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)....
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...…the NeighborJoining (NJ) algorithm that uses a matrix of pairwise distances estimated under the Jones–Thornton–Taylor (JTT) model for amino acid sequences or the Tamura and Nei (1993) model for nucleotide sequences (Saitou and Nei 1987; Jones et al. 1992; Tamura and Nei 1993; Tamura et al. 2004)....
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...The initial tree for the ML search can be supplied by the user (Newick format) 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)....
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37,524 citations
Cites methods from "The neighbor-joining method: a new ..."
...Distance matrices are clustered using UPGMA (11), which we ®nd to give slightly improved results over neighbor-joining (12), despite the expectation that neighbor-joining will give a more reliable estimate of the evolutionary tree....
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33,048 citations
Cites methods from "The neighbor-joining method: a new ..."
...For the Neighbor-Joining (NJ) method (Saitou and Nei 1987), memory usage increased at a polynomial rate as the number of sequences was increased....
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29,021 citations
Cites methods from "The neighbor-joining method: a new ..."
...the Neighbor-Joining method ( Saitou and Nei 1987 ), as the use of the MCL distances leads to a...
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...…from https://academic.oup.com/mbe/article-abstract/24/8/1596/1105236 by Zhejiang University user on 26 June 2018 Neighbor-Joining method (Saitou and Nei 1987), as the use of the MCL distances leads to a much higher accuracy (Tamura, Nei, and Kumar 2004)....
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References
15,840 citations
Additional excerpts
...Here, 2 represents a group of OTUs including all but 1 and 2, and Dlz and Dzz are the distances between 1 and 2 and 2 and 2, respectively (see Nei 1987, pp. 298-302, for an elementary exposition of this method)....
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10,262 citations
3,734 citations
"The neighbor-joining method: a new ..." refers methods in this paper
...After the nucleotide sequences for eight OTUs were produced, nucleotide differences were counted for all pairs of sequences, and the evolutionary distance (Jukes and Cantor 1969) was computed for each pair of OTUs....
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3,454 citations
"The neighbor-joining method: a new ..." refers methods in this paper
...Our procedure of estimating branch lengths is essentially the same as that of Fitch and Margoliash ( 1967)....
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3,332 citations