Figure 1From: CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomesAlignment construction protocol used in CGAT. The actual alignment calculation is carried out at the "all-all similarity search" step using one of the alignment engines. For "similarity search within each genome" in the upper-left rectangle, the same protocol is used as in the frame labeled "similarity search between genomes". See the text for details.Back to article page