Generating .xml File with binary coding

[wolfra...@gmail.com]

Hi All,

I'm somewhat new to beast, and I'm having difficulty creating a .xml file with BEAUti from my nexus file. I'm trying to use both DNA and Standard(binary) data. The nexus file works just fine in MrBayes, and it works fine with BEAUti when I remove the standard data. The error I get when I try to load the file is: Error parsing imported file: dr.evolution.io.Importer$ImportException: DATATYPE. The beginning of my nexus file looks as follows:

Begin DATA;
    Dimensions ntax=45 nchar=5768;
    Format datatype=MIXED(DNA:1-3278, STANDARD:3279-3444, DNA:3445-5749, STANDARD:5750-5768) gap=- INTERLEAVE=yes;
    Matrix

Any help regarding how to format the standard characters would be much appreciated!

Thanks,
Wolfgang Rahfeldt

[Andrew Rambaut]

Change the datatype to DNA or Nucleotide:

    Format datatype=nucleotide gap=- INTERLEAVE=yes;

Andrew

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Andrew Rambaut 

Institute for Evolutionary Biology | Centre for Infection, Immunity & Evolution 

Ashworth Laboratories, University of Edinburgh, Edinburgh, EH3 9JT, UK

contact – a.ra...@ed.ac.uk | http://tree.bio.ed.ac.uk | tel +44 131 6508624

[wolfra...@gmail.com]

Thanks! Now that I got my data into BEAUti, how do I implement a dollo model of site substitution for my binary data? I only see GTR, HKY, and TN93.

Thanks again in advance,
Wolfgang Rahfeldt