protmodel::BibliProt Class Reference
List of all members.
Member Function Documentation
| def protmodel::BibliProt::F84 |
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Felsenstein 1984.
Normalised such that the substitution rate on a stationnary
sequence is 1.
kappa: ratio transition/transversion
theta: equilibrium frequency of GC.
theta1: ratio of equilibrium frequency of A on equilibrium
frequency of AT
theta2: ratio of equilibrium frequency of G on equilibrium
frequency of CG
eta: rate (default=1)
| def protmodel::BibliProt::GTR |
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General Time-Reversible substitution model,
parametrization of Yang 1994.
Normalised such that the substitution rate on a stationnary
sequence is 1.
In proportion to the A<->G rate, the arguments are (default 1):
a: C<->T
b: A<->T
c: G<->T
d: A<->C
e: C<->G
theta: equilibrium frequency of GC.
theta1: ratio of equilibrium frequency of A on equilibrium
frequency of AT
theta2: ratio of equilibrium frequency of G on equilibrium
frequency of CG
eta: rate (default=1)
| def protmodel::BibliProt::HKY85 |
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Hasegawa Kishino Yano 1985
Normalised such that the substitution rate on a stationnary
sequence is 1.
kappa: transition/transversion rate
theta: equilibrium frequency of GC.
theta1: ratio of equilibrium frequency of A on equilibrium
frequency of AT
theta2: ratio of equilibrium frequency of G on equilibrium
frequency of CG
eta: rate (default=1)
| def protmodel::BibliProt::JC69 |
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Jukes and Cantor 1969.
Normalised such that the substitution rate on a stationnary
sequence is 1.
eta: rate (default=1)
| def protmodel::BibliProt::K80 |
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Kimura 1980.
Normalized such that the substitution rate on a stationnary
sequence is 1.
kappa: transition/transversion rate.
eta: rate (default=1)
| def protmodel::BibliProt::RN95 |
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Model first introduced in Rhetzky & Ney, 1995 and
developed in Schadt & al, 1998.
Normalized such that the substitution rate on a stationnary
sequence is 1.
The only hypothesis is that the transversion rates depend only
on the target nucleotides and not on the changed nucleotides.
alpha: A->G
beta: C->T
gamma: A->C=G->C
delta: C->A=T->A
epsilon: G->A
kappa: C->G=T->G
lambda: A->T=G->T
sigma: T->C
eta: rate (default=1)
| def protmodel::BibliProt::RN95s |
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intersection between L95 and RN95: The two hypotheses are
that the transversion rates are only dependent of the target
nucleotide, and strand symmetry.
Normalized such that the substitution rate on a stationnary
sequence is 1.
alpha: A->G=T->C
beta: C->T=G->A
gamma: A->C=G->C=T->G=C->G
delta: C->A=T->A=A->T=G->T
eta: rate (default=1)
| def protmodel::BibliProt::T92 |
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Tamura 1992.
Normalised such that the substitution rate on a stationnary
sequence is 1.
kappa: transition/transversion rate (default: 1).
theta: equilibrium frequency of GC (default: 0.5).
eta: rate (default=1)
| def protmodel::BibliProt::TN93 |
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Tamura and Nei 1993.
Normalised such that the substitution rate on a stationnary
sequence is 1.
kappa1: transition/transversion for A<->G.
kappa2: transition/transversion for C<->T.
theta: equilibrium frequency of GC.
theta1: ratio of equilibrium frequency of A on equilibrium
frequency of AT
theta2: ratio of equilibrium frequency of G on equilibrium
frequency of CG
eta: rate (default=1)
The documentation for this class was generated from the following file:
1.6.3