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Table 1 Examples of hierarchical model building in C4. Instead of building each model from scratch, most models are created in a modular fashion by making adaptions and additions to other models. This facilitates the building of complex models.

From: Automated generation of heuristics for biological sequence comparison

Model Components States Transitions
ungapped substitution matrix 3 3
Needleman-Wunsch (NW) ungapped with gap penalties 3 5
Smith-Waterman (SW) NW + local alignment scope 3 5
Smith-Waterman-Gotoh (SWG) SW + affine gap costs 5 9
est2genome SWG + intron models 10 24
protein2dna SWG + translation + frameshifts 6 13
protein2genome p2d + intron model 13 33