Full
model name: Dayhoff Empricial model.
Model type:
Amino acids.
Model
options:
- Fixed rates.
. Rates are
homogeneous (same for all sites in the data).
- Rate Variation.
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: t (for each branch of the tree) and,
if rate variation is selected as an option, the
corresponding distribution/hmm parameters.
Rate Matrix (1/1000 * the following matrix):

'*' is defined to be the
negative of the sum of all other row elements.
Each column
is multiplied by the equilibrium frequency of the amino acid
indicated above that column, and those frequencies are drawn
from the data below:
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