Full
model name: Muse-Gaut 1994
Model type:
Codon.
Model
options:
- Local.
Rates are homogeneous (same
for all sites in the data). Each branch has 2 parameters (synonymous
and non-synonymous rate).
- Global.
Rates are homogeneous (same
for all sites in the data). Each branch has 1 parameter (synonymous
rate). Non-Synonymous/Synonymous ratio is shared by all branches
in the tree.
- Global+Variation
Each branch has 1 parameter (synonymous rate). Non-Synonymous/Synonymous ratio
is shared by all branches in the tree. Different
sites may have different rates. The
user specifies how many different rate classes there should and
selects one of the available distributions
to be sampled. Distribution parameters are estimated.
- Rate Variation+HM. Similar to Rate Variation except that rates
at adjacent sites are correlated via a Hidden Markov Model
Independent
Parameters:
- Local.
synRate - synonymous rate, nonSynRate - non-synonymous
rate; (for each branch)
- Global.
synRate - synonymous rate (for each branch); R
- Non-synonymous/Synonymous ratio (shared by all branches in
the tree).
- Rate Variation (+HM).
Same as in the global setting plus the appropriate distribution parameters.
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).
- Local.

- Global, Rate Variation (+HM) :

Example of a one-step change: ACC->ATC;
more than one step: ACC->CGC.
refers to the observed
frequency of the target nucleotide that is changed in transition
from i to j. (E.g. it is the frequency of T in
the example above).
Equilibrium
frequencies of codons:
- MG94:
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.
- MG94w9:
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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