"Algebras/DotBracket/alg_ali_dotBracket.gap" is a special version of Algebras/DotBracket/alg_dotBracket.gap for alignments as input instead of a single sequence. The only difference is the type for the alphabet, i.e. the terminal parser.

Since algebra functions are commonly used by other algebras (Algebras/DotBracket/alg_dotBracket.gap, Algebras/DotBracket/alg_outside_dotBracket.gap, Algebras/DotBracket/alg_ali_dotBracket.gap and Algebras/DotBracket/alg_ali_outside_dotBracket.gap), they are outsourced in the files Algebras/DotBracket/algpart_dotBracket_basic.gap and Algebras/DotBracket/algpart_dotBracket_macrostate.gap.