Hi Stephanie,

What do mean by an average rate? HyPhy will estimate branch lengths for you (measured as expected subs/unit time), but and if you want the actual rate, you need to estimate the evolutionary time by other means (fossil record, molecular clock etc). Could you elaborate on the problem you are trying to solve?

Sergei

PS You may find section 2.2. of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login useful as background reading.

Hi Stephanie,

Do you have time information, i.e. are you talking about actual rates (e.g. subs/site/MY), or simply genetic distances (subs/site/unit time)?

In case it is the latter, then all you need is to perform a relative-ratio type analysis for your partitions. Averaging site-by-site estimates is not a good idea (mostly because they will have vastly differing variances), I would recommend simply obtaining a mean (per partition) estimate of substitution rates. Take a look at Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

This will allow you to estimate the ratio between substitution rates in your multiple regions.

To convert this to actual rates, you need more information (e.g. divergence time estimates)

HTH,
Sergei