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Table 1 Expanded Q matrix for ternary data

From: Comments on the model parameters in “SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models”

  0/- 0/0 0/1 1/- 1/1
0/- 0 NA NA NA NA
0/0 λ l -1 - λl 1 NA NA
0/1 \(\frac {\lambda _{l}}{2}\) \(\frac {\lambda _{d}}{2}\) −(λd+λl) \(\frac {\lambda _{l}}{2}\) \(\frac {\lambda _{d}}{2}\)
1/- NA NA NA 0 NA
1/1 NA NA λ d λ l λlλd
  1. Q(i,j) denotes transition from state i to state j. The transitions for which the entry is ‘NA’, are not allowed. In particular, we do not allow the transitions 0/- → 1/- or 1/- →0/- as a reflection of a simplifying assumption that a recurrent point mutation and deletion/LOH occurring at the same site is a very rare event. Furthermore, we do not model copy number gain.