sigma-align binary package in Ubuntu Precise amd64

 Sigma (“Simple greedy multiple alignment”) is an alignment program. It's
 algorithm and scoring scheme are designed specifically for non-coding
 DNA sequence.
 .
 It uses a strategy of seeking the best possible gapless local
 alignments. This happens at each step making the best possible alignment
 consistent with existing alignments. It scores the significance of the
 alignment based on the lengths of the aligned fragments and a background
 model. These may be supplied or estimated from an auxiliary file of
 intergenic DNA.

Source package