[Dart-announce] how to force --nointer to work?

[Rodrigo Gouveia-O. <ro...@cb...>]

Dear Users,

I am using xrate to estimate the  substitution rate matrices with 
several hidden classes. Then I use tkfemit to simulate data from these 
matrices. However, I need that each site in the alignment sticks to a 
class (that no columns in the alignment given by the inferclass option 
have more than one letter). That means that interclass rates have to be 
zero. That should be enforced by the --nointer option. Using this option 
lowers the rate, without setting it to zero, which still results in 
several mixed-class columns.So:

a) How do I make it be zero?  - I have tried providing a initial rate 
matrix with zeros but it wont converge. Small values always end up with 
mixed-class columns.

b)How can I access the likelihoods of the models? For instance, to 
choose between a 3 hidden class model and 2 hidden class model?

c)What do the capital and lower-case class assignments mean?

If you can help me with at least one of these questions, please do!

Thank you all,

Rodrigo

PhD student at www.cbs.dtu.dk