Figure 1

Flowgrams of INFERNAL (red, discussed here), our ADP re‐implementation ALTERNAL (blue, explained in Section ‘Recreating the core of INFERNAL ’) and the extension to ambivalent consensus structures aCM (green, introduced in Section ‘Ambivalent covariance models’). Input is the multiple sequence alignment(s) MSA and consensus structure(s) S S _cons for the construction of a model and RNA for homology search. Blue colored items are ADP components like grammars or algebras. The white box in aCM shall indicate that those operations are performed for each sub‐family.