Rev Language Reference

fnWAG(Simplex aaFrequencies)

aaFrequencies :	Simplex (pass by const reference)
	The stationary frequencies of the states.
	Default : [ 0.087, 0.044, 0.039, 0.057, 0.019, 0.037, 0.058, 0.083, 0.024, 0.048, 0.086, 0.062, 0.020, 0.038, 0.046, 0.070, 0.061, 0.014, 0.035, 0.071 ]

RateMatrix

The WAG model is an empirical model of amino acid replacement derived using an approximate maximum-likelihood method from 3,905 sequences across 182 protein families. It outperforms previous models like Dayhoff and JTT in terms of accuracy and likelihood for phylogenetic analysis, aiming to provide better evolutionary tree estimates and applications in sequence alignment, database searches, and protein structure prediction.

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

# WAG model with fixed frequencies
Q2 <- fnWAG()

• fnDayhoff
• fnJones
• fnLG