I'm not sure if this is a glitch with PolyGene or the ML estimator itself, but when calculating the Huang et al. 2015a ML estimator of relatedness all comparisons across ploidy (4, 5, and 6) are scored as 0.6125, regardless of actual relationship. I could understand 0 (still wrong), but why 0.6125? The moment estimator works fine with the same data, which are 325 SNP loci (input file attached).
sacramento.polygene.txt
I'm not sure if this is a glitch with PolyGene or the ML estimator itself, but when calculating the Huang et al. 2015a ML estimator of relatedness all comparisons across ploidy (4, 5, and 6) are scored as 0.6125, regardless of actual relationship. I could understand 0 (still wrong), but why 0.6125? The moment estimator works fine with the same data, which are 325 SNP loci (input file attached). sacramento.polygene.txt