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5454our manuscript.
5555
5656The ` search ` mode takes as input an $m \times n$ frequency matrix $F$ and outputs
57- an $n$-clonal tree that best fits the frequency matrix. * Important note: the search
58- command requires a root vertex specified with the ` -f/--assigned-root ` flag.*
57+ an $n$-clonal tree that best fits the frequency matrix. ** Important note: the search
58+ command requires a root vertex specified with the ` -f/--assigned-root ` flag.**
5959By default this root vertex is set to be $0$. When the root vertex is unknown,
6060it suffices to append an extra column to the beginning of the frequency matrix
6161and specify the root as $0$.
6262
6363The ` regress ` mode
6464takes as input an $m \times n$ frequency matrix $F$ and an $n$-clonal
6565tree $\mathcal{T}$ and outputs the minimum value of
66- ` \lVert F - UB_{\mathcal{T}} \rVert_1 ` over all usage matrices $U$.
66+ $ \lVert F - UB_ {\mathcal{T}} \rVert_1$ over all usage matrices $U$.
6767
6868### Input format
6969
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