This new automated chimerism software, ChimerMarker™, integrates analysis operations for initial donor/recipient compatibility and post engraftment longitudinal studies. The new software is compatible with outputs from major capillary electrophoresis platforms as well as commercially available STR and custom chemistries. ChimerMarker software can be used to monitor chimerism in allogeneic and autologous stem cell transplant, hematopoietic stem cell transplant, bone marrow transplant, and peripheral blood stem cell transplant. The program preferences include labeling of peak ratios by height or area, with multilineage capabilities for chimerism analysis of T cells, B cells, and other cell type populations, which may indicate graft-versus-host disease or graft rejection. Case-specific panels are automatically constructed using donor recipient allele calls.