PPGtk is a program for the analysis of population genomic data collected in polyploids.

Information for installing and running PPGtk can be found here.

• Estimate per-site allele frequency under Hardy-Weinberg equilibrium [freqs model].
• Estimate per-site inbreeding/disequilibrium coefficient and allele frequency [diseq model].

In the near future, I hope to add these features to the software:

• Estimate subgenome allele frequencies for allopolyploids [alloSNP model]. See my Evolution 2016 slides for a description of the model: link.

• Genotype estimation.

• Use genotype likelihoods instead of read counts.