Let p(a b.u v)denote the true probability of observing the quartet topology a b.u v in gene trees generated according to the MSC model. We define MSC-based double, single, and all-pairs anchored distance matrices \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$D^{*}_{u,v}, D^{*}_{v}$\end{document}Du,v∗,Dv∗, and D ∗, respectively on leaf-sets \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$\mathcal {L}-\{u,v\}, \mathcal {L}-\{v\}$\end{document}ℒ−{u,v},ℒ−{v} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$\mathcal {L}$\end{document}ℒas: 5\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $$\begin{array}{@{}rcl@{}} D^{*}_{u,v} [a,b] &=& -\ln p(ab.uv) \end{array} $$ \end{document}Du,v∗[a,b]=−lnp(ab.uv)