Full
model name: Goldman-Yang 1994
Model type:
Codon.
Model
options:
- S/N independent Rates are
homogeneous (same for all sites in the data). Each branch has
2 parameters (synonymous and non-synonymous rate).
- S/N shared
Rates are homogeneous (same
for all sites in the data). Each branch has 1 parameters (non-synonymous
rate). Synonymous/Non-synonymous ratio is shared by all branches
in the tree.
- S/N independent +Gamma Different
sites may have different rates. The user specifies how many different
rate classes there should be. Gamma distribution with unknown
shape parameter alpha is used to evaluate rates for each class.
The shape parameter of the gamma distribution is estimated as
a model parameter. Each branch has 2 parameters (synonymous and
non-synonymous rate).
- S/N shared
+Gamma Different sites
may have different rates. The user specifies how many different
rate classes there should be. Gamma distribution with unknown
shape parameter alpha is used to evaluate rates for each class.
The shape parameter of the gamma distribution is estimated as
a model parameter. Each branch has 1 parameters (non-synonymous
rate). Synonymous/Non-synonymous ratio is shared by all branches
in the tree.
Independent
Parameters:
- S/N independent mu - non-synonymous rate, R - Synonymous/Non-synonymous
ratio for the branch; (for each branch); kappa - transition/transversion
ratio (shared by all branches).
- S/N shared
mu -
non-synonymous rate (for each branch); R - Synonymous/Non-synonymous
ratio; kappa - transition/transversion ratio (shared by
all branches).
- S/N independent+Gamma mu - non-synonymous rate, R - Synonymous/Non-synonymous
ratio for the branch; (for each branch); kappa - transition/transversion
ratio (shared by all branches). alpha - the shape parameter
of the gamma distribution (shared by all branches in the tree).
- S/N shared +Gamma mu - non-synonymous rate (for each branch); R
- Synonymous/Non-synonymous ratio; kappa - transition/transversion
ratio (shared by all branches). alpha - the shape parameter
of the gamma distribution (shared by all branches in the tree).
Rate Matrix
Entries:
Note: the rate matrix will have the same dimension
as the number of non-stop codons in the genetic code which is
being used be the analysis (61 for Universal Code).

Example of one-step changes: ACC->ATC
(transition), ACC->AGC (transversion);
more than one step: ACC->CGC.
refers to the equilibrium
frequency of codon j.
Equilibrium
frequencies of codons:
- GY94:
Equilibrium frequency of codon ijk
is the product of observed frequencies of nucleotides
which compose the codon, normalized by a factor to account for
the presence of stop codons.
- GY94w9:
Equilibrium frequency of codon ijk
is the product of observed frequencies of nucleotides
which compose the codon, which are tabulated by 1st,2nd and 3rd
positions in the codon (i.e. 3 sets of 4 frequencies are used,
one for each position in the codon), normalized by a factor to
account for the presence of stop codons.
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