Implementing the Mk substitution model with BEAST and BEAGLE

What steps will reproduce the problem?
1. Use BEAUti to make an XML file with HKY model
2. Edit out the HKY model blocks and relevant ops and replace it with the Mk 
model following the testLewisMk.xml template 
(https://code.google.com/p/beast-mcmc/source/browse/trunk/examples/release/testX
ML/testLewisMk.xml?r=4413)
3.  Open the XML using BEAST/1.7.4 and BEAGLE

What is the expected output? What do you see instead?

I expect the run to begin and finish without erroring out, because that is what 
it does when I run it without the BEAGLE module.  However, I get the following 
error when using BEAGLE:

Constructing 4-state datatype
Parsing error - poorly formed BEAST file, test.xml:
The '<lewisMk>' element with id, 'lewisModel', is incorrectly constructed.
The following was expected:
Exactly one ELEMENT of name frequencies REQUIRED containing
    Exactly one ELEMENT of type FrequencyModel REQUIRED

Again, the XML runs fine without BEAGLE.

What version of the product are you using? On what operating system?
Beast/1.7.4, Beagle/1090;  Linux Centos 5.5 OS.

Please provide any additional information below.
I found the description of this same problem but with the TN93 model and not 
Mk, located under Issue 571.  Comment #7 says this is not a BEAGLE issue and 
that the issue was resolved by updating BEAST itself.  However, my file runs 
fine without BEAGLE...  If it is indeed a BEAST issue, would it be possible to 
update BEAST to accomodate the Mk model?

Original issue reported on code.google.com by roxana.c...@gmail.com on 3 Sep 2013 at 8:19

Attachments:

test.xml

evolvedmicrobe / beast-mcmc

Implementing the Mk substitution model with BEAST and BEAGLE #695