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Model
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Batch language command
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'Model' is used to define an evolution model by specifying substitution rate matrix and equilibrium frequencies.
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Syntax
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Model model_name = (rate_matrix_ident,freq_vector_ident,);
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Notes
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Optional boolean mult_flag is used to indicate whether rate matrix elements should be automatically multiplied by the appropriate equilibrium frequency. Default is 1(true), and if the value of the flag is 0 (false), then the equilibrium frequencies should be integrated into the rate matrix explicitly.
Rate matrix must be a square matrix. The diagonal elements are ignored if defined, and reset to ensure reversibility. Frequencies matrix must be a column vector of the same dimension as the rate matrix. The frequency vector must be supplied, even when it is included in the structure of the rate matrix (as in F84).
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Examples
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See files in the 'Examples' directory.
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Last modified: 8/19/2002 |
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