SoftGenetics - Software PowerTools for Genetic Analysis






Forensic & Medical Mitochondrial DNA Analysis

Developed in collaboration with leading forensic and medical laboratories, GeneMarkerHTS software provides rapid analysis of multiple samples using consensus and motif alignments:

  • Unique motif alignment technology
    o Automates the requirements set by The DNA Commission of the International Society for Forensic Genetics
    o Fulfills the forensic alignment recommendations.
    o Provides recognition and proper assignment of motifs and indels consistent with phylogenetic and forensic considerations
  • Consensus alignment
    o To the preloaded Revised Cambridge Reference Sequence or to other references

Read the article Validation of NGS for mitochondrial DNA casework at the FBI Laboratory



Motif alignment reduces manual edits for forensic alignment

Figure 1: GeneMarkerHTS software has an extensive, preloaded forensic motif file as well as a motif editor to assist labs in adding new motifs.


Automatic Features Include:

  • Three alignment algorithms that best suit the analysis needs:
    o Initial Alignment to a reference genome (Revised Cambridge Reference Sequence is preloaded into GeneMarkerHTS)
    o Adjust alignment with motifs to ensure the alignment is consistent with forensic variant reporting
    o Adjust alignment using the consensus; improving alignment around indels
  • Analysis across the origin
  • Forensic or standard nomenclature
  • Maintain health privacy with an administrative option that blocks display of disease associated positions

Analysis Results Include:

  • Consensus sequence, Variants, SNPs, Indels
  • Depth of coverage graphics
  • Consensus sequence aligned to reference (IUPAC nomenclature)
    o Whole mtDNA genome, spanning the origin
    o Specified areas of interest, such as control region, HV1, HV2
  • Read pile-up (with depth and direction indicators)
  • Compare multiple samples in single view
    o Synchronized view - scroll and zoom multiple samples
  • Comparison viewer - table with sample-to-sample and variant composition

GeneMarkerHTS Software Viewing Options:

  • Users can customize color-coding for nucleotides and highlight edits
  • ‘Global’ and ‘Zoom’ views for the whole mtDNA genome alignment
    o The Global View shows the depth of coverage with forward read coverage in blue and reverse read coverage in red
    o The Zoom View allows users to zoom-in on the range displayed in the pile-up




Figure 2: Global view (left) and Zoom view (right).

  • View up to 4 samples simultaneously




Figure 3: Synchronized viewing of multiple samples

  • Compare analysis results of multiple samples




Figure 4: Sample-to-sample comparison (top) and variant comparison of all samples in the project (bottom)


GMHTS Software can Export a Variety of Reports:

  • Consensus sequence
  • Variant reports – SNPs, heteroplasmy, and insertions and deletions
  • Variant reports are EMPOP (EDNAP mtDNA Population Database) compatible

Minimum Recommended processing hardware: 64-bit Windows OS 12 GB RAM 2.4GHzDual Quad Core Processor. 

SoftGenetics - Software PowerTools for Genetic Analysis


  • Mitochondrial DNA Analysis
  • Autosomal and Y-STR Genotypes and SNPs

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