GeneMarker Software: Editions and STR Workflow

GeneMarker is Windows-based genotype analysis software from SoftGenetics that reads fragment-analysis files from capillary electrophoresis instruments and turns them into allele calls. Researchers use it for short tandem repeat (STR) profiles, MLPA, SNaPshot and microsatellite work. This guide explains what the software is used for, how its editions differ, and the exact window and menu names in the STR workflow documented in Promega’s user manual.

What GeneMarker is used for in research

SoftGenetics describes GeneMarker as genotype analysis software and positions it as an alternative to Applied Biosystems GeneMapper and to MRC Holland’s Coffalyser.Net. Its product page lists these application areas (SoftGenetics, GeneMarker page, checked 2026-11-07):

Clinical research: MLPA, MS/MLPA, microsatellite instability (MSI), repeat expansion (HTT, DMPK, ALS), Fragile X, trisomy, loss of heterozygosity (LOH), ARMS and OLA (cystic fibrosis), haplotype analysis and single base extension (SBE/SNaPshot).
Ecology and agriculture: microsatellites (SSR, STR, VNTR), kinship, cluster analysis, AFLP, T-RFLP, TILLING/EcoTILLING and MLVA.

The software accepts output from ABI PRISM and Applied Biosystems SeqStudio instruments and from Promega Spectrum Compact CE systems, as well as custom primers and commercial 4-6 dye chemistries. For the upstream steps that produce these files, see our guide to Sanger sequencing, which uses the same capillary electrophoresis instruments, and the overview of gel electrophoresis for the separation principle.

Which edition does this guide cover?

Several editions share the GeneMarker name, and their documentation is not interchangeable. The general GeneMarker product page covers many applications (MLPA, SNaPshot, microsatellite and others). Promega distributes a SoftGenetics-developed edition for human identification, called GeneMarker HID Software for Spectrum CE Systems, documented in Promega technical manual TM555 (revision 1/23). The step-by-step workflow below follows TM555. For MLPA or SNaPshot, follow SoftGenetics’ own application notes and training material for that edition.

Edition or source	What it documents	Where to read it
GeneMarker (SoftGenetics)	General genotype analysis across clinical research, ecology and agriculture applications	softgenetics.com/GeneMarker.php
GeneMarker HID for Spectrum CE Systems (Promega)	STR analysis for forensic casework, databasing, missing persons and relationship testing on ABI 3130, 3130xl, 3500 and 3500xL and Spectrum CE instruments	Promega technical manual TM555

Install or access (official sources only)

Use the vendor’s own channels. SoftGenetics offers a free trial through the “Free Trial” and “Download Trial Software” links on its GeneMarker page. The software runs on Windows, in versions that are still within Microsoft Extended Support.

For the Promega edition, TM555 (section 2) gives these requirements and steps:

Recommended computer: Windows 10, dual-core processor, 4 GB RAM and 256 GB of disk. Lower specifications may operate but have not been tested at Promega.
Download: at www.promega.com/gmhid/. After purchase, a Software Registration Document gives download instructions and license password(s). The license can be local or network.
Trial: a 35-day trial can be installed without a license. Extract the compressed folder, double-click the installer .exe, accept the License Agreement with “I Agree”, select “Main” in Choose Components, then click Next.

Prices are set by the vendors and are not covered here.

Step-by-step: analysing an STR project (GeneMarker HID, Promega TM555)

These steps use the window and button names from TM555 revision 1/23. Check them against the manual for the version you have installed.

Open the program. Use the desktop shortcut or the Start menu. The menu bar has six menus: File, View, Project, Applications, Tools and Help.
Open your data. Use the Magic Wizard (“Start your project”), the Open Data toolbar icon, or File > Open Data. The “Open Data Files” window has the buttons Add, Remove, Remove All and Add Folder, plus a Dyes button.
Use supported files and one chemistry per project. Accepted types are Promega .fsa and .promega, and Applied Biosystems .fsa and .hid. Keep a single STR chemistry in each project; the manual’s example is PowerPlex Fusion 6C and PowerPlex Y23 data imported into separate projects. Each file shows a load status of Completed or Failed.
Check the raw data. After loading, the Main Analysis window shows the raw data. Click the Run Project icon to open the Run Wizard.
Select a template. The Run Wizard has three screens. The first is Template Selection. Templates store analysis parameters, and preloaded templates exist for many Promega STR kits. Select the Analysis Panel, the Size Standard Template and the Size Standard Color.
Verify the panel and size standard before analysing. Confirm that the panel and size standard exist for your kit and match its marker size ranges, dye channels, stutter percentages, peak amplitude thresholds and size-standard fragment sizes.
Choose the sizing method. The software offers two sizing methods; “Local Southern” is the one commonly used for STR data. Saturation detection and repair is also available.
Save and run. Save stores any template changes; OK applies the settings. The Data Processing Event Log then labels each sample Completed (blue) or Failed (red). Click OK to continue to the Main Analysis window.

Genotyping is done against an allelic ladder, as the manual describes. Multiplex chemistries of this kind are discussed in our guide to multiplexed PCR.

Output and how to read it

After processing, the Main Analysis window shows four main elements (TM555 section 5):

Sample File Tree: includes an “Allele Call” folder.
Electropherogram Chart: the trace for the selected sample and dye.
Report Table: the allele table.
Project Summary Bar: quality metrics for the project.

Toolbar functions you will use most are Print Report, Size Calibration, Show Chart/Table, Save Peak Table, Call Allele and the Marker drop-down. Save Peak Table exports .xlsx, tab-delimited .txt or .csv, with options for Filter Delete Peaks and Exclude Report Header. Call Allele lets you re-analyse by sample, marker or dye.

For interpretation, the manual points to specific chapters: 5.F for re-analysing, 10.A for Profile Quality and its Quality Indicators (10.A.4), 10.B for the Contamination Check, and chapter 13 for the limit of detection (13.A), stutter ratio (13.B) and height ratio (13.C). Post-genotyping tools in the same software include expert system review, database creation and profile searching, kinship and population statistics.

Troubleshooting

These items follow the behaviour TM555 describes in its workflow, which has no dedicated troubleshooting chapter.

A file shows Failed on load. The manual treats a corrupt file or one that cannot be loaded as Failed. Confirm the file is one of the accepted types.
A sample shows Failed (red) in the Data Processing Event Log. Check the size standard color and size standard template selected in the Run Wizard.
Allele calls look wrong or missing. Return to Template Selection and check that the Analysis Panel and size standard match the kit used for the run.
Two chemistries in one project. Import them into separate projects.
Flagged quality. Review the Project Summary Bar and the Profile Quality chapter (10.A) before accepting calls, and use Call Allele to re-analyse a sample, marker or dye after correcting settings.

Free alternatives

Software	Maintainer	Scope and licensing, as stated by the maintainer
OSIRIS	NCBI	Public-domain, free, open source STR analysis software for clinical, forensic and research use, validated as an expert system for single-source samples (ncbi.nlm.nih.gov/osiris, checked 2026-11-07).
Coffalyser.Net	MRC Holland	Free MLPA data analysis software. A newly installed server is activated with a free license from the download page; licenses must be renewed periodically and remain free (support.mrcholland.com, checked 2026-11-07).

The two cover different jobs: OSIRIS is for STR profiles, Coffalyser.Net for MLPA. For related lab tools, see Bioanalyzer vs TapeStation for nucleic acid sizing and SnapGene vs Benchling for sequence design software.

FAQ

What is GeneMarker software?

It is SoftGenetics’ Windows genotype analysis software for capillary electrophoresis fragment data, used for STR, MLPA, SNaPshot, microsatellite and related analyses.

Is there a GeneMarker tutorial?

The numbered workflow above follows the Promega TM555 manual for the HID edition. For MLPA and other applications, use the SoftGenetics application documentation for that edition.

Is there GeneMarker training?

The manufacturers’ manuals are the documented learning resource; this guide points to the specific TM555 chapters for quality review.

Can I try GeneMarker for free?

SoftGenetics offers a free trial through its trial request page, and the Promega edition has a 35-day trial installable without a license.

Does GeneMarker run on Mac?

SoftGenetics describes GeneMarker as Windows-based. OSIRIS lists Mac and Windows versions.

Sources

Promega. GeneMarker HID Software for Spectrum CE Systems User Manual TM555, revision 1/23, checked 2026-11-07: Promega technical manual page.
SoftGenetics. GeneMarker software, checked 2026-11-07.
NCBI. OSIRIS, checked 2026-11-07.
MRC Holland. Coffalyser.Net support article, checked 2026-11-07.