Evaluation of GeneMarker® HTS for improved alignment of mtDNA MPS data, haplotype determination, and heteroplasmy assessment.

•GeneMarker® HTS was developed as a comprehensive tool for analysis of mtDNA MPS data.•A novel alignment and motif file approach was used for development of GeneMarker® HTS.•Successful haplotype determination for 500 CR sequences with GeneMarker® HTS.•Successful heteroplasmy assessment for 500 CR sequences with GeneMarker® HTS.•Minimal manual analysis required when using GeneMarker® HTS.