Flowchart and graphical user interface of ConStruct. Steps are numbered as in the text. The graphical user interface (grey part) shows results of a structural alignment for IRES regions of CrP-like viruses ; for a full view and further details of this alignment see Fig. 3. The main windows of CONSTRUCT are the "Consensus Dotplot" and the "Alignment Editor". The top-right triangle in the consensus dotplot shows thermodynamic base pairing probability of individual sequences (blue/green) and thermodynamic consensus matrix (red), the horizontal and vertical bars denote gaps; the lower-left triangle shows the MI (as a measure of covariance) normalized by pair entropy and a threshold of tCV = 50 % applied. Predicted structures may be displayed in several representations and formats. On the right side, two possible representations are shown. The Circles plot (upper window) shows the consensus structure as predicted by maximum weighted matching (MWM); consensus pairing probability is color-coded from white to red. The crossing arcs represent pseudoknots. Below the "Structural Alignment Output" is shown. From top to bottom: ten sequences [with background colors green for loops, red for consensus base pairs, pink for consensus base pair changes (covarying pairs), and white for non-base pairs in paired regions], the consensus sequence, and the consensus structure in bracket-dot notation and character-encoded (both with background colors from white to red proportional to sequence conservation resp. pairing probability). For an overview of colors used in CONSTRUCT see Table S4 in Additional file 1.