Full
model name: Hasegawa et.al., 1985.
Model type:
Nucleotide
Model
options:
- Local.
Rates are homogeneous (same
for all sites in the data). Each branch has 2 parameters (transition
rate and transversion rate).
- Global.
Rates are homogeneous (same
for all sites in the data). Each branch has 1 parameter (transversion
rate). Transition/transversion ratio is shared by all branches
in the tree.
- Global+Gamma
Each branch has 1 parameter (transversion
rate). Transition/transversion 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 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 -
transversion rate, b - transition rate; (for each branch)
- Global.
a -
transversion rate (for each branch); R - transition/transversion
ratio (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):

with the vector representing
nucleotide frequencies (proportions) from the data. '*' is defined
to be the negative of the sum of all other row elements.
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