average sequence length n character frequencies /* UndefinedMacro: latex($f=(f_1,\ldots,f_\ell)$) */
mutation guide tree //**T**// (edge length, standard: 1) * OR
sequence distance /* UndefinedMacro: latex($d_{AV}$) */ (generate binary T over average pairwise sequence distance)
mutation matrix /* UndefinedMacro: latex($M,\ \ \ell\times\ell$) */ (pairwise mutation frequencies for substitutions insertion / deletion probability functions * /* UndefinedMacro: latex($\begin{array}{lclll}p_{ins}&/&p_{del}&&\mbox{probabilities}\\\ell_{ins}&/&\ell_{del}&&\mbox{indel lengths}\end{array}$) */
mutation <del>probability</del> likelihood vector /* UndefinedMacro: latex($\nu,\ \ |\nu|=n$) */ (specify sequence motifs)