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Figure 1 | BMC Bioinformatics

Figure 1

From: Using the nucleotide substitution rate matrix to detect horizontal gene transfer

Figure 1

The nucleotide substitution rate matrix summarizes the instantaneous rate of change from each of the four nucleotides to each of the other four nucleotides. Each row of the rate matrix must sum to zero, and only the diagonal elements can be negative; and therefore each diagonal element is equal in magnitude but opposite in sign to the sum of the other three elements in its row. Presentation of the rates in this way is due to N. Sueoka (pers. comm.) [52, 53]. As is the convention, we estimate the rate matrix is using only the bases at the third codon position, which approximate neutral evolution. Thus, A3 refers to A at the third codon position, and so forth.

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