ArrayAssist Copy Number Software (Stratagene) is a guided workflow system that enables researchers to manipulate and analyze the massive data sets generated by chromosomal copy number microarrays. The Copy Number package is Stratagene’s most recent application on the ArrayAssist platform, which includes ArrayAssist Expression and ArrayAssist Exon. All applications have earned GeneChip compatible status with the Affymetrix platform. They will soon be provided as universal binaries, able to run natively on the latest Intel-based Macintosh computers, and are compatible with Mac OS X, Windows, and Linux. The new software supports the identification of biomarkers for cancer, degenerative disease and developmental disorders by highlighting chromosomal amplifications and deletions. Biologists can compare their experimental data in ArrayAssist Copy Number with a reference genome using ArrayAssist’s integrated genome browser, a feature of all ArrayAssist applications, and can map biological pathways for a comprehensive understanding of the relevant relationships in their system with the integration of Stratagene’s PathwayArchitect platform.