Hi Jeff,

In Branch-site REL, the mean omega is estimated using a simple evolutionary model (one omega per branch), and artificially capped at 10 (as you noticed). It is meant to serve as a starting value for the optimization for BS REL, and should not be used for inference.

The average of omega estimates from the multiple rate model is NOT going to equal the mean in general. You should compute the weighed average, if you want to get a more comparable value (omega1 * prob (omega = omega1) + omega2 * prob (omega = omega2) ...), but even then don't expect equality. This is because averaging point estimates does not take variance into account. If you have omega = 10000 inferred from 1% of sites, the confidence bounds on that 10000 are going to be very wide.

Generally, you should NOT use point estimates, but rather the results of hypothesis testing (for some discussion on the matter see  Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login). If you wish to estimate the mean omega at a branch, it is better to do this directly (e.g. with a simple MG94 local model), and not by transforming point estimates of individual rate classes under a more complex model.

Sergei