Fig. 4.

SPhyR more accurately recovers the simulated matrices $B^{*}$ and trees $T^{*}$ than SCITE and SiFit. Given the same input matrix D, each method inferred an output matrix B and phylogenetic tree T. (a–c) The tradeoff between the false negative rate (FNR) and the false positive rate (FPR) for each matrix B output by each method. (d–f) Three different measures that assess similarity between $T^{*}$ and T in terms of character states occurring on the same branch (d), on distinct branches (e) and on the same edge (f) in both $T^{*}$ and T