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).