Hi,

In speedtest.bf (in Examples/BatchFiles) I do not really understand the use of synRate. Why every entry of the Q-matrix is multiplied by synRate? I run the file without synRate and I noticed that the likelihood has decreased and the values of the parameters have changed? I also run another version of that file where synRate is considered as a global parameter. The result is not very far from when it is considered as local parameter. Would you please explain to me the reason behind those facts?

Thanks in advance,
Elyrajo

Dear Elyrajo,

For a long answer, please read the 1st part of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

The short answer is that synRate is the product of the synonymous substitution rate and the branch length (they are confounded, this is a standard shortcoming of all time reversible substitution models).

Removing synRate has the effect of fixing the length of every tree branch at some arbitrary value (hence a worse likelihood), and making it global makes all branches have the same length, but now estimated from the data (better than not having it at all, but worse than estimating each branch length individually as should be done).

Cheers,
Sergei

Dear Sergei,

Thanks for your reply. You were talking about synonymous substitution rate. However I have noticed that synRate is multiplied to all of the entries of the matrix.
What section in first part especially should I read in hyphydocs.pdf? I must acknowledge that I did not read it thoroughly so far.

Cheers,
Elyrajo