This maximization is carried out using the standard Viterbi algorithm14. Segments of continuous copy number C are assigned a lod score reflecting the log-likelihood of the path including the event (Si = {F1i, Ci, Ci, Ci, ... F2i} versus the log-likelihood of the path excluding the event Si = {F1i, F1i, F1i, F1i, ... F2i} or Si = {F1i, F2i, F2i, F2i, ... F2i}), where F represents the copy number of the flanking segment (Supplementary Methods).
