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.