Full model
name: Tamura and Nei, 1993
Model type:
Nucleotide
Model
options:
- Local.
Rates are homogeneous (same
for all sites in the data). Each branch has 3 parameters (transversion
rate and 2 transition rates, one for purines, the other for pyrimidines).
- Global.
Rates are homogeneous (same
for all sites in the data). Each branch has 1 parameter (transversion
rate). 2 transition/transversion ratios are shared by all branches
in the tree.
- Global+Variation
Each branch has 1 parameter (transversion rate).
2 transition/transversion 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 -
transversion rate, b - purine transition rate, c
- pyrimidine transition rate; (for each branch)
- Global.
a -
transversion rate (for each branch); R1 - transition/transversion
ratio for purines; R2 - transition/transversion ratio
for pyrimidines; (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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