Multiple alignment visualization. Sockeye is simultaneously showing alignments for regions around the first exon of the Huntington's Disease gene (HD) from LAGAN (top four sequence tracks) and ClustalW (bottom four sequence tracks). The sequence tracks in order are (1) mouse, (2) rat, (3) human, (4) Fugu, (5) mouse, (6) rat, (7) human, and (8) Fugu. For the LAGAN algorithm, the start of translation of the HD gene in each species aligns perfectly. For the ClustalW algorithm, the start of translation for the first exon of the Fugu ortholog is misaligned. The Ensembl exon annotation includes the untranslated region. Ensembl-curated repeats are shown in red; gaps are shown in gray. This image shows how Sockeye can be used for comparative genomics and comparative algorithmics.