Tree reconstruction in the presence of doublet samples. (A) Cell lineage tree with doublets (gray boxes). (B) Mutation tree with true sample attachment. Doublet samples (s₃, $s_3^{\mathrm{\prime }}$) and (s₄, $s_4^{\mathrm{\prime }}$) each attach to two different nodes. (C) Mutation matrix with combined mutation states for the doublet samples. Mutations are counted as present in a doublet sample if present in at least one of the cells. (D) A tree with a recurrence of mutation M₂ and no doublets is an alternative explanation for the mutation matrix in C.