Clustering HERV proviruses according to their expression patterns. All EST sequences matched by the HERV-K family were aligned to all HERV proviruses present in the query set (31 HERV-K proviruses and 1 representative member for each of the HERV-H, W and E family). Alignment scores were normalized to obtain bit scores. A color-code ranging from red (low) to white (high) was used to represent bit scores (lower panel). Bit scores lower than the threshold of 36 are represented in black. HERV proviruses were clustered, using average-linkage agglomerative hierarchical clustering, based on the binary distances between pairs of proviral sequences (upper panel).