DBA

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Richard Durbin, Niclas Jareborg, and Ewan Birney's DNA Block Aligner program available here. From the web site:

Dna Block Aligner (DBA) aligns two sequences under the assumption that the sequences share a number of colinear blocks of conservation separated by potentially large and varied lengths of DNA in the two sequences. The aim was that this was a very sensible thing to do with syntenous regions of non coding DNA between say mouse and human, for example, the upstream regions of a gene from mouse and human, or the conserved intron of a human - chicken gene. The conserved blocks may be regions important for regulation of the gene.
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