Sanger data analysis

We offer a wide portfolio of Applied Biosystems™ software solutions for viewing and interpreting your Sanger sequencing and fragment analysis results.  Learn about our free tools and commercially available products below.

Looking for software support? 
Visit our Capillary Electrophoresis Software Support Center.

Data collection software

Software Description Operating system requirements

Applied Biosystems™ Data Collection Software

Download software patches
Upgrade to the latest version

Data Collection Software is an integrated software for instrument control, data collection, quality control, base-calling, and size-calling of samples. Operation of the instrument is dependent on this software.

Windows™ 7

Sanger sequencing software

Viewer
Software Description Operating system requirements

Applied Biosystems™ Sequence Scanner Software  v2.0

Download

Sequence Scanner Software allows you to view, edit, print, and export data generated using Applied Biosystems™ genetic analyzer instruments after data has been processed by Sequencing Analysis Software.

Windows 7

Applied Biosystems™ Quality Check Module

Sign in

The Quality Check (QC) module evaluates trace quality. The easy-to-interpret analysis summary gives a snapshot of Sanger sequence trace quality. The Trace Details page allows you to evaluate and edit traces as needed. The Flag Settings page allows you to adjust quality thresholds. Free access on Thermo Fisher Cloud
Primary analysis tool
Software Description Operating system requirements

Applied Biosystems™ Sequencing Analysis Software v6.0

Download software patches

Sequencing Analysis Software uses a base-caller algorithm that performs base calling for pure and mixed base calls.  The software analyzes, displays, edits, saves, and prints sample files that are generated from Applied Biosystems DNA analyzers and genetic analyzers.

Windows 7
Secondary analysis tool
Software Description Operating system requirements

Applied Biosystems™ Minor Variant Finder Software

Download trial version

Minor Variant Finder Software enables 5% somatic variant detection using Sanger sequencing. The improved sensitivity makes Sanger sequencing a fast, cost effective, and accurate way to call low-frequency somatic variants where the number of relevant targets is limited.

Windows 7 SP1, 32-bit or 64-bit or Windows 10 Pro, 64-bit

Applied Biosystems™ SeqScape™ Software v3.0

Download trial version

SeqScape Software is a resequencing package designed for mutation detection and analysis, SNP discovery and validation, pathogen sub-typing, allele identification, and sequence confirmation. It provides library functions for comparison to a known group of sequences, as well as features to assist with 21 CFR Part 11 compliance (Security, Audit and electronic signature features), which can be important in clinical research labs. Windows 7

Applied Biosystems™ Variant Reporter™ Software v2.0

Download trial version
Variant Reporter Software is designed for reference-based and non-reference-based analysis such as mutation detection and analysis, SNP discovery and validation, and sequence confirmation. The robust algorithms will call SNPs, mutations, insertions, deletions, and heterozygous insertions⁄deletions for data generated using Applied Biosystems genetic analyzers. Windows 7

Applied Biosystems™ Variant Analysis (VA) Module

Sign in

The Variant Analysis (VA) Module provides fast analysis of Sanger sequencing data. The VA Module can automatically retrieve reference sequences from the genomic database, report variants with genomic coordinates, and report genomic annotations for SNPs. With highly overlapped forward/reverse strands, the VA Module reports very high sensitivity for SNP calls. The VA Module also reports and exports variant files in standard .vcf format. There is no software maintenance required from users. Free access on Thermo Fisher Cloud

Applied Biosystems™ Next Generation Confirmation (NGC) Module

Sign in

The Next-Generation Confirmation (NGC) Module lets users compare results from standard NGS variant files with results from Sanger sequencing instruments within the Thermo Fisher Cloud environment.
Critical decisions often require validation of NGS results using robust Sanger sequencing. The NGC module provides fast analysis of AB1 files and reports variants in genomic coordinates. The results are automatically annotated with known SNPs from the current genomic database.
Free access on Thermo Fisher Cloud

Applied Biosystems™ MicroSEQ™ ID Microbial Identification Software

Download trial version

MicroSEQ ID Microbial Identification Software is a tool for identification of bacteria and fungi. The software analyzes data generated using a MicroSEQ chemistry kit and an Applied Biosystems capillary-based genetic analyzer. Windows 7

Applied Biosystems™ MicrobeBridge™ Software

Download trial version

 
MicrobeBridge Software is a streamlined, desktop software solution that connects DNA sequences generated on Applied Biosystems Sanger sequencers with the Centers for Disease Control and Prevention (CDC)’s MicrobeNet™ database for bacterial identification using 16S rRNA gene sequencing analysis. There is no need for local database setup, so computer resources are easily developed. Windows 7
Fragment analysis software
Sizing software
Software Description Operating system requirements

Applied Biosystems™ Peak Scanner™ Software

Download

Peak Scanner Software is a DNA sizing software that can either be downloaded for free or purchased for free as a software kit.

Use this software to perform DNA fragment analysis, separate a mixture of DNA fragments according to their sizes, provide a profile of the separation, and precisely calculate the sizes of the fragments. The software allows you to view, edit, analyze, print, and export fragment analysis data generated using Applied Biosystems genetic analyzers. 

Windows 7

Applied Biosystems™ GeneMapper™ Software 5

Download trial version
Download software patches

GeneMapper Software is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. This software specializes in multi-application functionality, including amplified fragment length polymorphism (AFLP™) analysis, loss of heterozygosity (LOH), microsatellite, and SNP genotyping analysis. In addition, the security and audit features help users meet 21 CFR 11 requirements. Windows 7
Primer design tool
Software Description Operating system requirements

Applied Biosystems™ Primer Designer™ Tool

Access tool

The free, online Primer Designer Tool allows you to search for the right PCR/Sanger sequencing primer pair from a database of ~650,000 predesigned primer pairs for resequencing the human exome and human mitochondrial genome.

Web tool

Applied Biosystems™ Methyl Primer Express™ Software v1.0

Download software

Methyl Primer Express Software v1.0 enables you to design high-quality PCR primers for methylation mapping experiments. Simply cut and paste in your region of interest. The tool searches for CpG islands and simulates bisulfite modification of DNA in silico.  
Minor Variant Finder
Sanger sequencing chemistry guide