3.4.4 Rate across site distribution

From version 0.4.0, BppSuite uses the keyval syntax for specifying the distributions of substitution rate across sites.

rate_distribution = {rate distribution description}

Specify the rate across sites distribution.

The rate distribution is set to have a mean of 1. The following distributions are currently available:

Constant

Uses a constant rate across sites.

Gamma(n={int>=2}, alpha={float>0})

A discretized gamma distribution of rates, with n classes, and a given shape, with mean 1 (scale=shape).

Invariant(dist={rate distribution description}, p={real[0,1]})

A composite distribution allowing a special class of invariant site, with a probability p.