Rev Language Reference

fnLG - LG (Le and Gascuel) Amino Acid Substitution Rate Matrix

Generates a rate matrix based on the Le and Gascuel (LG) substitution model for amino acid evolution.

Usage

fnLG(Simplex aaFrequencies)

Arguments

aaFrequencies : Simplex (pass by const reference)
The stationary frequencies of the states.
Default : [ 0.079, 0.056, 0.042, 0.053, 0.013, 0.041, 0.072, 0.057, 0.022, 0.062, 0.099, 0.065, 0.023, 0.042, 0.044, 0.061, 0.053, 0.012, 0.034, 0.069 ]

Return Type

RateMatrix

Details

The LG model is an empirical model of amino acid replacement derived from large-scale protein alignments. It refines substitution rate estimation by explicitly considering site-specific rate variation.

Example

# LG model with estimated frequencies
pi ~ dnDirichlet( rep(1,20) )
Q := fnLG(pi)

# LG model with fixed frequencies
Q2 <- fnLG()

See Also

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