$F\in {ℝ}_{\ge 0}^{m\times (\ell +r)}$	$f_{p,s}$ is mixed copy number of variant s in sample p
$Q\in {\{0,1\}}^{\ell \times r}$	$q_{b,s}$ is 1 iff breakpoint b is in segment s
$G\in {\{0,1\}}^{\ell \times \ell }$	$g_{s,t}$ is 1 iff breakpoints s and t are mated pairs
$n\in \mathbb{N}$	number of leaves in the phylogenetic tree
$c_{max}\in {\mathbb{N}}_{>2}$	maximum allowed sub-clonal copy number for
	breakpoints and segments
${\lambda }_1\in {ℝ}_{\ge 0}$	regularization term to weight total tree cost
${\lambda }_2\in {ℝ}_{\ge 0}$	regularization term to weight breakpoint consistency