Can I use SNAPP with diploid data?

Yes, under the assumption that sites or markers are unlinked. As usual, a SNP which is homozygous for allele 1 is coded by '2', a SNP which is homozygous fir allel '0' is coded by '0', and a heterozygous SNP is coded by '1'. Note that diploid individuals are effectively treated as two haploid individuals, with heterozygous alleles allocated at random.

How do I make SNAPP treat the data as dominant AFLP data?

Either:

1. In BEAUTI, select the `Dominant' check box in the `Mutation Model' tab pane, or
2. In the XML file, look for the tag determining the likelihood distribution within the tag determining the posterior distribution:

  
<distribution id="treeLikelihood.aflp_25" spec="snap.likelihood.SnAPTreeLikelihood" dominant="true" data="@snap.aflp_25" pattern="coalescenceRate" tree="@Tree.aflp_25">
   <siteModel id="MutationSiteModel.aflp_25" spec="SiteModel">
        <parameter id="mutationRate" estimate="false" name="mutationRate">1.0</parameter>
        <parameter id="shape" estimate="false" name="shape">2.0</parameter>
        <parameter id="proportionInvariant" estimate="false" name="proportionInvariant">0.0</parameter>
        <substModel id="MutationModel" spec="snap.likelihood.SnapSubstitutionModel" coalescenceRate="@coalescenceRate" mutationRateU="@u" mutationRateV="@v"/>
    </siteModel>
</distribution>

Insert the option `dominant = "true"' as above.

How can I do species delimitation with SNP/AFLP data?

See Bayes Factor Delimitation (*with genomic data)

Can BEAUti process VCF data?

BEAUti can only handle nexus, fasta, and alignments in BEAST 1 and 2 xml format.

There is a Perl script vcf2nex.pl that may or may not help converting a vcf file to nexus, which then can be imported into BEAUti.