1. Alphabet /* UndefinedMacro: latex($\Sigma,\ \ |\Sigma|=\ell$) */
2. root sequence s
   • OR

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)