The use of dyes in STR product analysis is dealt with in course: Amplified DNA Product Separation, Fluorescent Detection Module. Selection of dyes is generally based upon instrument compatibility and spectral overlap. The effective use and development of different colored dyes (that can be used together) results in an output consisting of organized peaks in a variety of colors, rather than of a series of indistinguishable peaks. In general, the dyes used to label primers for forensic DNA analysis are fluorescent

and emit color at different wavelengths.

Although the dyes are different colors, their spectra can overlap because the wavelengths that determine color occur simultaneously, not discretely. 

Due to spectral overlaps, a matrix must be run with each instrument. A matrix is created by running each color separately on the instrument. The instrument then compares the individual colors to one another. The matrix file is represented in table format.

The matrix file allows the instrument software to normalize the fluorescence between the colored dyes and creates a virtual filter, separating the colors for sample analysis.⁰¹

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