Designed and written by Dr. Oliver Serang
(with advice from Marcelo Mollinari)
in Junina 2011 while he was a visiting scientist at USP/ESALQ
in the lab of Prof. Antonio Augusto Franco Garcia.

SuperMASSA is a handy (+free!)
graphical Bayesian inference tool for genotyping polyploids
(compatible with Sequenom MASSArray and Illumina GoldenGate).

Model: F1 Cross
Hardy-Weinberg
Don't use population-level
information

Print predicted genotypes:

Draw genotype scatterplot:

Histogram of genotype frequencies:

Use exact MAP:

Naive posterior reporting threshold:

Ploidy range (low:high:step):

σ range (low:high:step):

Data file:

F1 parent data
(optional; only for F1 model):

Details can be found in the paper:
O. Serang, M. Mollinari, and A. A. F. Garcia. (2012) "Efficient Exact Maximum a Posteriori Computation for Bayesian SNP Genotyping in Polyploids.
PLoS ONE 7(2): e30906. doi:10.1371/journal.pone.0030906

It's easy! Format your data like this: names, x-intensity, y-intensity
Demo 1: (1,1) x (1,1) Demo 2: (0,2) x (1,1)

Sugarcane data from the paper can be found here

*Don't worry, you're data is not stored (besides, when would I find the time to use it?!); you're secret's safe with me, Spider-Man!