3.4.1 Setting up the substitution model
- model = {model description}
- A description of the substitution model to use, using the keyval syntax.
From version 0.4.0 of BppSuite, the model specification uses a
completely new syntax, based on the keyval (key = value) scheme. The
old option files will hence not be compatible with new version of the
software. The new syntax however is hopefully more intuitive, and more
generalizable, so that few changes are expected when new models will
be built. The substitution model is a function, potentially including
parameters. The following table lists the set of usable functions, and
their parameters.
Many models have a set of optional parameters denoted here as
"equilibrium frequencies" that are used to initialize the parameters
of the model related with the equilibrium frequencies. These options
are:
- initFreqs=values({real]0,1[},...,{real]0,1[})
- The equilibrium frequency is set equal (as much as possible) to the
given frequencies. Those frequencies are given in the same order as
the alphabet, and they must sum 1.
- initFreqs=observed
- The equilibrium frequency is set equal (as much as possible) to the
observed frequencies.
- initFreqs.observedPseudoCount={integer}
- a peusocount integer added to all counts of letters (or words), when
the frequencies are computed from observed data.