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:

  
    
       
          
                    ...
          
        
    
  

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.