StarBeast3 template – gene ploidy panel

The ploidy (copy number) for each gene can be configured here. Ploidy is based on the mode of inheritance for each gene and is typically a whole number or half; autosomal and nuclear: 2, X: 1.5, Y: 0.5, most viral: 1, mitrochondrial: 0.5. The default is 2. Using the wrong ploidy results in population sizes being estimated incorrectly, and only affects estimate of the tree through the prior on population mean.