**rate factor**: the relative evolutionary rate for each site.

The average rate factor across sites is 1.

Two methods for estimation of site-specific rate factor are available:

1. alignment-based rate factor (less time and lower precision)

- rate factor is estimated empirically based on conservation of a site

2. maximum likelihood rate factor (more time and higher precision)

- rate factor is estimated by
maximizing the likelihood of residues at a site given a tree

If neither of them is selected, the uniform rate factor is used (rate factor is 1 for
every site).