morph-models

[Anne Kupczok]

Hi,

I am trying to use morphological models with BEAST2. Therefore I loaded the MM package.

I am able to import a nexus file as an alignment into BEAST (attached). However I was not able to transform this file into a file that is accepted by "Add Morphological Data".

The MK model is working when I import the file, however I would like to use the MKv model. As I understand the MKv model is only implemented in the MM package. Any suggestions which information is missing in my nexus file to make it work with MM is highly appreciated.

Thanks,
Anne

[Alexandra Gavryushkina]

Dear Anne,

There are constant characters in the file you provide. That means that you can not use the Mkv model which assumes there are no constant characters in the matrix. 

If you want to keep the constant characters and use Mk model then you also need to specify in CHARSTATELABELS how many possible states a character can take. BEAUti automatically partitions the matrix in groups of characters having the same number of possible states which is either taken from CHARSTATELABELS or calculated from the character. Character that can only take one state are not allowed as they don't bring any information. Note, that it is different from having a constant character which could take more than one state. Then if there is no 

CHARSTATELABELS and there is a constant character, BEAUti can not assign the number of possible states greater than one. You can see an example of  CHARSTATELABELS  in this file: 

https://github.com/CompEvol/morph-models/blob/master/examples/nexus/penguins_morph.nex

you can also look at this paper:

https://academic.oup.com/sysbio/article/46/4/590/1629695/Nexus-An-Extensible-File-Format-for-Systematic

[Anne Kupczok]

Thanks, that is the problem!
I was only thinking about all-0 characters, but of course all-1 characters are constant too.