Full
model name: Muse-Gaut 1994 with rate matrix extensions.
Model type:
Codon.
Model
options:
- Rate matrix options.
The user selects the type of nucleotide rate multipliers to graft onto
the MG94 rate matrix (see example below). The specification is
done the same way as in the
Custom 4x4 model.
This step may add up to 5 shared rate parameters (depending on the user's
choice: B,C,D,E,F)
to the model, to compensate for nucleotide substitution bias, which
may not be accounted for in the classic MG94.
- 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 (in addition to nucleotide rate substitution shared 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. Example with 010010 (HKY85) nucleotide rates.
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 (transition): 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:
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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