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

[Ian H. <ih...@bd...>]

Dear Rodrigo,

as mentioned in a previous mail I'm in the middle of a move this week & so
sorry if my answers are terse...

> 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.

This is a bug that seems to result from the way xrate treats mixture
models (with no inter-class substitution) as a special case of dynamic
class models (where the class can be substituted). The long-term fix for
this will be in the next version of xrate, which will include much more
flexible mixture models.

Until then, it should certainly be possible to patch the code so that the
inter-class rates are forced to zero if "--nointer" is specified. I can't
do this until next week, but if you want to try hacking the code yourself,
the relevant file is "dart/src/em_matrix.cc"

> 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?

Set the log level to 7 or lower (see my previous email), pending a more
user-friendly way of doing this...

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

(stalling for time) have you checked that your input sequence data
aren't mixed-case? Most dart sequence I/O code preserves the case.

Best wishes,
Ian