Full
model name: Equal Input model for amino acids.
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: a (for each branch of the tree) and,
if rate variation is selected as an option, the
corresponding distribution/hmm parameters.
Rate Matrix
Entries:

i,j range from 1 to 20 and denote the ij cell
denotes the instantaneous rate of change from amino acid i
to amino acid j. Numerical ordering of the amino
acids is based on the sorted alphabetical order of their one
character abbreviations (see Amino
acid character table).
'*' is defined
to be the negative of the sum of all other row elements.
denotes
the proportion of amino acid j as observed in the
data.
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