Hello, you could compute a matrix of pairwise Hamming distances between your individuals' alleles calls (i.e. see https://datagy.io/python-hamming-distance) and cluster them (with PHYLIP neighbor or another tree reconstruction tool working from distance matrices (MEGA does that too, but its input file format is somewhat unfriendly).

If you have many missing data calls, and you want to correct the pairwise distances to account for them, you could look at how it is implemented in: Galpern P, Manseau, M, Hettinga P, Smith K, and Wilson P. (2012) allelematch: an R package for identifying unique multilocus genotypes where genotype error and missing data may be present. Molecular Ecology Resources 12:771-778

Hth.