Quantitative genetics (genetics of complex traits) is a field of research that studies the effects of genome on the phenotypic traits in organisms. One of the approaches to follow the phenotype inheritance is the analysis of mitochondrial DNA (mt-DNA), which is conserved only in maternal line. One of the tools for that purpose has been the Magellan software [1], which has found its application in the analysis of population pedigrees in livestock, as well as the selection of individuals best suited for mt-DNA sequencing. Here, we present recent development of the software. The user friendliness has been improved through the implementation of graphical user interface, as well as through the integration of existing modules in the command line interface. The new visualisation module allows for a greater user insight in the structure of important parts of pedigrees. The computational cost of the sampling procedure has been greatly reduced through the implementation of two efficient algorithms. Besides mt-DNA polymorphisms and maternal lineages, the software is now capable of applying the same procedures to Y-chromosome polymorphisms and paternal lineages. A new module has been added for the analysis of pertinent SNPs found in populations, as well as for finding deleterious mutations in individuals’ mitogenomes. These advances will enable the software to find a broader audience in the scientific community and wider applications in its field.