Figure 6.

The traceback() algorithm. Reconstruction of the optimal parse by tracing back through trellis links. Parameters are the selected right-terminus signal s and its chosen phase ω. Returns a stack of signals constituting the optimal parse, with the top signal at the beginning of the parse and the bottom signal at the end. exon_length(p, s) denotes the number of coding nucleotides between p and s. The procedure operates by iteratively following the highest-scoring predecessor link from the current signal, adjusting the current phase as necessary when a trellis link corresponding to a coding feature is traversed.