We have noticed [43] that DIALIGN is more sensitive than TRACKER in general. This is due to detection of smaller and less significant fragments with DIALIGN compared to the larger, contiguous fragments returned by BLASTZ. The combination of BLASTZ and an anchored version of DIALIGN appears to be a very promising approach for phylogenetic footprinting. It makes use of the alignment specificity of BLASTZ and the sensitivity of DIALIGN. A combination of anchoring at appropriate genes (with maximal weight) and BLASTZ hits (with smaller weights proportional e.g. to – log E values) reduces the CPU requirements for the DIALIGN alignment by more than an order of magnitude. While this is still much slower than TRACKER (20 min vs. 40 s) it increases the sensitivity of the approach by about 30 – 40% in the Fugu example, Table 1. Work in progress aims at improving the significance measures for local multiple alignments. A more thorough discussion of anchored segment-based alignments to phylogenetic footprinting will be published elsewhere.