Morphological/Binary models

[ostratodd]

Is anyone working on adding to BEAST morphological models, such as
Lewis' Mk model?

[Alexander Alekseyenko]

The Lewis' Mk model is already sort-of in Beast. You would use a
general substitution model to set that up. In addition to the Mk model
you may want to consider using Stochastic Dollo model, which is also
in Beast with examples. I could work with you to help set up the
analysis. It would also be good if we could work together on a short
tutorial on how to set up morphological models in Beast.

Cheers,

Alex

[Vidette Botha]

Hi Alex,

Just wondering if you have made a tutorial on how to set up morphological models in Beast,
and if not, do you perhaps know where i can find one for Beast v1.7.5.?
My data set contains both phylogenetic and descrete morphological traits,
I am however not sure how to set up my analysis. 
Any help will be appreciated.

Thanks,
Vidette

[Alexander Alekseyenko]

Dear Vidette,

There isn't a single tutorial on this. But you can look for ideas on how to implement your model in the following test XML: testLewisMk.xml and testBinaryDollo.xml. You can combine the molecular and morphological partitions in a single analysis.

Cheers,

Alex

[William Gearty]

Hi Alex,

I'm trying to set up a combined *BEAST analysis of morphological and molecular data and am trying to set up the Lewis model in Beauti v 2.1.2.

Is there a tutorial or example file for such an analysis?

I have already set the models for the many genes in the analysis, but I receive the following error when I try to set the model for the morphological data:

Could not add entry for substModel

Any thoughts?

Thanks,

Will 

[William Gearty]

Anyone have any ideas regarding this?