Full
model name: Kimura 3 substitution type model (1981)
Model type:
Nucleotide
Model
options:
- Local. Rates are
homogeneous (same for all sites in the data). Each branch has
3 parameters (transition rate and 2 types of transversion rates).
- Global.
Rates are homogeneous (same
for all sites in the data). Each branch has 1 parameter (transition
rate). 2 transversion/transition ratios are shared by all branches
in the tree.
- Global+Variation Each branch has 1 parameter
(transition rate).
2 transversion/transition ratios are shared by all branches in
the tree. Different
sites may have different rates. The user specifies how many different
rate classes there should be 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.
a -
A<->C,G<->T transversion rate, b - transition
rate, c - A<->T,G<->C transversion rate; (for
each branch)
- Global.
b -
transition rate (for each branch); R1 - tranversion/transition
ratio for A<->C,G<->T; R2 - tranversion/transition
ratio for A<->T,G<->C; (shared by all branches in
the tree).
- Rate Variation (+HM).
Same as in the global setting plus the appropriate distribution parameters.
Rate Matrix:
- Local.
- Global, Rate Variation (+HM):

'*' is defined to be the negative of the sum
of all other row elements.
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