Invariable Sites model
Note by Celeste: Is this invariable or invariant?
The Invariable Sites model is the simplest method to add discrete rate partitions to a model of sequence evolution. There are two rate categories, with relative rate parameters of 0 (meaning the site is invariable) and 1.
wr, the probability that a site i belongs to a variable or invariable class, is estimated from the data.
The model's main parameter, pinvar, stands for the proportion of sites that are invariable. It needs to be less than the proportion of sites that are constant, because there is a probability such a site is variable but hasn't experienced a substitution because of randomness.