3.5.1.2 Protein models

JC69

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

DSO78

Protein substitution model, using the dcmutt implementation of Kosiol and Goldman 2005. See the Bio++ description.

JTT92

Protein substitution model, using the dcmutt implementation of Kosiol and Goldman 2005. See the Bio++ description.

WAG01

Protein substitution model, from Whelan & Goldman 2001. See the Bio++ description.

LG08

Protein substitution model, from Le & Gascuel 2008. See the Bio++ description.

LLG08_EX2([relrate1={real]0,1[}, relproba1={real]0,1[}])

Protein substitution model, from Le, Lartillot & Gascuel 2008. See the meaning of the variables in the Mixture model below. See the Bio++ description.

LLG08_EX3([relrate1={real]0,1[}, relrate2={real]0,1[}, relproba1={real]0,1[}, relproba2={real]0,1[}])

Protein substitution model, from Le, Lartillot & Gascuel 2008. See the meaning of the variables in the Mixture model below. See the Bio++ description.

LLG08_EHO([relrate1={real]0,1[}, relrate2={real]0,1[}, relproba1={real]0,1[}, relproba2={real]0,1[}])

Protein substitution model, from Le, Lartillot & Gascuel 2008. See the meaning of the variables in the Mixture model below. See the Bio++ description.

LLG08_UL2([relrate1={real]0,1[}, relproba1={real]0,1[}])

Protein substitution model, from Le, Lartillot & Gascuel 2008. See the meaning of the variables in the Mixture model below. See the Bio++ description.

LLG08_UL3([relrate1={real]0,1[}, relrate2={real]0,1[}, relproba1={real]0,1[}, relproba2={real]0,1[}])

Protein substitution model, from Le, Lartillot & Gascuel 2008. See the meaning of the variables in the Mixture model below. See the Bio++ description.

DSO78+F([theta={real]0,1[}, theta1={real]0,1[}, theta2={real]0,1[}, ... ,"equilibrium frequencies"])

Protein substitution model, using the dcmutt implementation of Kosiol and Goldman 2005 and free equilibrium frequencies. The thetaX are frequencies parameters, where X is 1 to 19. Parameter theta1 is the proportion of A, theta2 is the proportion of R over (1-A), theta3 the proportion of N over (1-A-R), etc. See the Bio++ description.

JTT92+F([theta={real]0,1[}, theta1={real]0,1[}, theta2={real]0,1[}, ..., "equilibrium frequencies"])

Protein substitution model, using the dcmutt implementation of Kosiol and Goldman 2005 and free equilibrium frequencies. See the Bio++ description.

WAG01+F([theta={real]0,1[}, theta1={real]0,1[}, theta2={real]0,1[}, ..., "equilibrium frequencies"])

Protein substitution model, from Whelan & Goldman 2001, and free equilibrium frequencies. See the Bio++ description.

LG08+F([theta={real]0,1[}, theta1={real]0,1[}, theta2={real]0,1[}, ..., "equilibrium frequencies"])

Protein substitution model, from Le & Gascuel 2008, and free equilibrium frequencies. See the Bio++ description.

Empirical(name={chars}, file={path})

Build a protein substitution model from a file in PAML format, and use ’name’ as a namespace for parameters.

Empirical+F(name={chars}, file={path}, [theta={real]0,1[}, theta1={real]0,1[}, theta2={real]0,1[}, ..., "equilibrium frequencies"])

Build a protein substitution model from a file in PAML format, and use free equilibrium frequencies. ’name’ will be used as a parameter namespace, including for frequencies.