Microarrays were scanned using a GenePix 4000B Scanner (Molecular Devices) and data analysed using the maximum likelihood method developed at LLNL, extensively described elsewhere [19] . Additional stringency criteria were applied to exclude bacterial sequences and viruses having fewer than 20% of probes detected out of those expected. Briefly, probes were classified as detected if the intensity exceeded a threshold equal to the 99 th percentile of intensities for negative control probes, except that one sample was analysed using the 95 th percentile. Targets in an internal database of 43 705 viral sequences, developed at LLNL [19] , were screened against the stringency criteria; an unconditional log-odds score for presence of each remaining target was computed, and targets having log-odds scores less than 5 were excluded. A greedy forward selection algorithm was applied to find the collection of targets most likely to be present in the sample. At every forward selection step, a conditional log-odds score was computed for each remaining target, representing its potential contribution to the log-likelihood conditioned on the presence of the previously selected targets; the target having the largest conditional log-odds was selected and added to the collection. The resulting conditional and unconditional log-odds scores were plotted in a bar graph format [19] , where the conditional log-odds scores shows the contribution from a target that cannot be explained by another, more likely target above it, and the unconditional score illustrates that some very similar targets share a number of probes, so that multiple targets may be consistent with the hybridization signals.