| DNA Methylation Analysis | Methyl Primer Express® Software v1.0 | Design methylation-specific primers (MSP) and bisulfite sequencing primers (BSP). | Genetic Analyzers | Download |
| qPCR Protein expression analysis | ProteinAssist™ Software (pre-release 1) | Import Ct files exported from real-time systems to view and analyze protein expression assay data for relative quantitation. | Real-time PCR Systems | Download |
| DNA Sequencing | Sequence Scanner Software v1.0 | View, edit, print and export sequence data generated using the Applied Biosystems Genetic Analyzers. | Genetic Analyzers | Download |
| DNA Sequencing | Color Space Mapping Tool | Enables you to map SOLiD color space reads to whole human genomes. Available as source code. | SOLiD™ Analyzer | Download |
| DNA Sequencing | SOLiD™ System Analysis Pipeline Tool | Allows you to map color space reads to large or small genomes, to place and annotate paired reads, and to call SNPs. Available as source code. | SOLiD™ Analyzer | Download |
| DNA Sequencing | SOLiD™ Alignment Browser | A genome annotation viewer and editor which is based on the Apollo Genome Annotation Curation Tool. | SOLiD™ Analyzer | Download |
| DNA Sequencing | Small RNA Analysis Pipeline Tool | A small RNA SOLiD™ System Analysis Pipeline for human whole genome alignment of small RNA sequencing data with tag counting features. Available as source code. | SOLiD™ Analyzer | Download |
| DNA Sequencing | General Feature Format (GFF) Conversion Tool | Enables you to consolidate reference-aligned SOLiD™ data into a standard format (General Feature Format). Available as source code. | SOLiD™ Analyzer | Download |
| DNA Sequencing | Sequence Read Format Conversion Tool | Enables you to convert native SOLiD™ data into a community-driven standard (Short Read Format) for NCBI submission. Available as source code. | SOLiD™ Analyzer | Download |
| Fragment Analysis | Peak Scanner™ Software v1.0 | The free Peak Scanner™ Software performs DNA fragment analysis, which separates a mixture of DNA fragments according to their sizes, provides a profile of the separation, and precisely calculates the sizes of the fragments. The software allows you to view, edit, analyze, print, and export fragment analysis data generated using the Applied Biosystems Genetic Analyzers. | 3100 Genetic Analyzer
3100-Avant™ Genetic Analyzer
3130 and 3130xl Genetic Analyzer
730 and 3730xl DNA Analyzer | Download |
| SNP Genotyping | SNPbrowser™ Software v4.0 | Select optimal sets of SNPs for association and fine mapping studies by visualizing SNPs in their genomic context using linkage disequilibrium maps and putative haplotype blocks. | Genetic Analyzers, Real-Time PCR Instruments | Download |
| SNP Genotyping | Mouse SNPbrowser™ Software | Enables efficient and easy selection of mouse SNP sets to discriminate between strains of interest, with specific applications in genotype/phenotype mapping and strain variation. | Genetic Analyzers, Real-Time PCR Instruments | Download |
| SNP Genotyping | TaqMan® Genotyper Software | Provides a state-of-the-art genotype calling algorithm, intuitive user interface, enhanced Study-based analysis features, and high call rates and accuracy. | Applied Biosystems Real-Time PCR Systems (excluding 7300 System), and OpenArray® Genotyping Instrument. | Download |
