The software application developed (FLiPARS 2.0) efficiently automates the computationally intensive process of mtDNA mixture deconvolution by linkage phase analysis. The current release of FLiPARS 2.0 has been successfully run on a variety of Windows, Mac OS, and Linux operating systems. The Graphical User Interface has been designed to be intuitive and user friendly. The base-calling and alignment algorithms also allow the sequence being analyzed to be edited in accordance with the judgment and experience of a skilled practitioner. These results were achieved with the completion of three major research objectives. One objective was to develop a robust software application and user friendly graphical interface to import and deconvolve sequence electropherogram files. The second objective was to test the accuracy of the software application on a broad range of mixture ratios and mixed base positions using both reference and casework-type samples. The third objective was to analyze the performance and accuracy of the software application and make appropriate revisions to resolve any anomalies. 12 figures and 31 references