3.4.1.1 Nucleotide models

JC69

The Jukes and Cantor model. This model has no additional parameter. See the Bio++ description.

K80([kappa={real>0}])

The Kimura 2 parameters model. kappa is the transition over transversion ratio. Default: kappa=1. See the Bio++ description.

F84([kappa={real>0}, theta={real]0,1[}, theta1={real]0,1[},theta2={real]0,1[} ,"equilibrium frequencies"] )

Felsenstein's 1984 substitution model, with transition/transversion ratio and 4 distinct equilibrium frequencies, set using three independent parameters: theta is the GC content, theta1 is the proportion of G / (G + C) and theta2 is the proportion of A / (A + T or U). See the Bio++ description.

HKY85([kappa={real>0}, theta={real]0,1[}, theta1={real]0,1[}, theta2={real]0,1[} ,"equilibrium frequencies"])

Hasegawa, Kishino and Yano 1985's substitution model. The model is similar to F84, but with a different implementation. The kappa parameter used here is comparable to the one in K80. See the Bio++ description.

T92([kappa={real>0}, theta={real]0,1[} ,"equilibrium frequencies"])

Tamura 1992's model for nucleotides, similar to HKY85, yet assuming that the frequencies of A = T/U and G = C. See the Bio++ description.

TN93([kappa1={real>0}, kappa2={real>0}, theta={real]0,1[}, theta1={real]0,1[}, theta2={real]0,1[} ,"equilibrium frequencies"])

Tamura and Nei 1993's model, similar to HKY85, but allowing for two distinct transition/transversion ratios. See the Bio++ description.

GTR([a={real>0}, b={real>0}, c={real>0}, d={real>0}, e={real>0}, theta={real]0,1[}, theta1={real]0,1[}, theta2={real]0,1[} ,"equilibrium frequencies"])

The General Time-Reversible substitution model. Parameters a, b, c, d, e are the entries of the exchangeability matrix. See the Bio++ description.

L95([beta={real>0}, gamma={real>0}, delta={real>0}, theta={real]0,1[}, theta1={real]0,1[}, theta2={real]0,1[} ,"equilibrium frequencies"])

The strand-symmetric model of Lobry 1995, for nucleotides. See the Bio++ description.