Abstract: Methods, apparatus, and software for identifying sets of genomic oligonucleotides that identify a viral family and for determining sets of probes and primers that can be used to identify members of viral families in a sample are provided. In one embodiment, the method of the present invention includes normalizing viral genomic oligonucleotide sequence data from at least one viral family, and identifying at least one oligonucleotide sequence that is unique to each viral family. An array of the identified oligonucleotide sequences is made. Primers provided by the present invention are used to amplify viral family genomic sequences in a biological sample of interest, and probes provided using the present invention, e.g., attached to an array or biochip, are then used to detect the presence of the corresponding virus(es) present in the sample by hybridization.