TO USE THE GARLI GAP MODELS

1. PUT YOUR ALIGNMENT IN THIS DIRECTORY
    (for tutorial, tutorialData.fas)

2. TO PREPARE THE GAP CODED DATA FOR GARLI, EXECUTE EITHER 
    prepareFastaData.sh myAlignment.fas
or
    prepareNexusData.sh myAlignment.nex

3. TO ANALYZE THE CREATED DATASETS, EXECUTE
    runGarli.dna+gapModels.sh
    TO RUN DNA alone, DNA+DIMM and DNA+Mkv MODELS
OR
    ./runGarli.indelMixtureOnly.sh
    TO ONLY RUN DIMM MODEL

-Note that the DIMM output tree will contain a taxon 
    called ROOT, which is essentially an outgroup that
    indicates the inferred root.  This can be deleted.
    Note that to load this tree into a program like
    PAUP, the alignment must also contain a dummy taxon
    name ROOT.  A script will try to make this for you
    if possible, or your might need to manually do so.


LET ME KNOW OF ANY ISSUES
Derrick Zwickl
garli.support@gmail.com

