The rapid generation of mutation data matrices from protein sequences
Citations
39,110 citations
Cites methods from "The rapid generation of mutation da..."
...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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27,771 citations
Cites methods from "The rapid generation of mutation da..."
...…in a benchmark using simulated protein sequences (Löytynoja et al. 2012) generated by INDELiBLE (Fletcher and Yang 2009), when we tested a more stringent scoring matrix, JTT 1PAM (Jones et al. 1992) with weaker gap penalties than the default, the benchmark scores were considerably improved....
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...2012) generated by INDELiBLE (Fletcher and Yang 2009), when we tested a more stringent scoring matrix, JTT 1PAM (Jones et al. 1992) with weaker gap penalties than the default, the benchmark scores were considerably improved....
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...The ––bl, ––jtt, and ––tm options mean BLOSUM (Henikoff S and Henikoff JG 1992), JTT (Jones et al. 1992), and a transmembrane model (Jones et al....
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...The ––bl, ––jtt, and ––tm options mean BLOSUM (Henikoff S and Henikoff JG 1992), JTT (Jones et al. 1992), and a transmembrane model (Jones et al. 1994), respectively....
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...For example, in a benchmark using simulated protein sequences (Löytynoja et al. 2012) generated by INDELiBLE (Fletcher and Yang 2009), when we tested a more stringent scoring matrix, JTT 1PAM (Jones et al. 1992) with weaker gap penalties than the default, the benchmark scores were considerably improved....
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16,261 citations
Cites background or methods from "The rapid generation of mutation da..."
..., 1978) and JTT (Jones et al., 1992) models for proteins are also available and run quickly, requiring about 3 min to analyze a data set comprising 50 mammalian sequences and 1,729 sites (F....
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...The Dayhoff (Dayhoff et al., 1978) and JTT (Jones et al., 1992) models for proteins are also available and run quickly, requiring about 3 min to analyze a data set comprising 50 mammalian sequences and 1,729 sites (F. Delsuc, pers. com.)....
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12,124 citations
12,003 citations
Cites background from "The rapid generation of mutation da..."
...(22), Sop (gap opening penalty, de®ned below) is 2....
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...(22), fa is the frequency of occurrence for amino acid a calculated by Jones et al....
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...(22) with two modi®cations; 20 amino acids are grouped into six physico-chemical groups (24), and the number Tij of 6-tuples shared by sequence i and sequence j is counted....
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References
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