3.5.1 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.