I just run TreeMix and I got weird results, I thought it might be because of missing data so I am wondering whether TreeMix handles missing data, and how it does it. The command line I used is:

treemix -i input_file.gz -o out_treemix

Missing data in my input_file.gz is given as 0,0 (zero counts for both alleles), see subset of my sampleset:

sample1 sample2 sample3 sample4 sample5
13,27 6,20 3,2 3,3 0,0
3,3 0,0 1,2 2,4 2,3
1,2 1,2 0,2 2,2 0,6
0,0 0,0 0,2 1,3 0,4
0,0 0,0 1,7 0,0 1,7
0,0 0,0 0,3 0,0 0,0
0,5 0,0 1,4 2,4 1,4

What I get as 'weird' results is a tree with no distances (all samples in the same level with no distance from root, so it is a vertical line) and in the residuals plot I get 0 for all comparisons (the plot is completely white) but not for the diagonal, which is yellow-red.

Thanks