===== Input Parameters =====

  - Alphabet /* UndefinedMacro: latex($\Sigma,\ \ |\Sigma|=\ell$) */ 
  - 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)