NAME

       makeHKY - Generates an HKY tree model, given kappa (the transition/transversion

DESCRIPTION

       Generates  an  HKY  tree model, given kappa (the transition/transversion rate ratio).  The
       equilibrium base composition and either  a  branch  length  or  a  complete  tree  can  be
       specified by the options described below.

OPTIONS

       --gc, -g <val>

              Define  base composition according to specified G+C composition, assuming P(A)=P(T)
              and P(C)=P(G).  Default is 0.4.

       --pi, -p <pi_A,pi_C,pi_G,pi_T> Override  --gc  and  define  base  composition  explicitly.
              Values will be renormalized to ensure they sum exactly to one.

       --branch-length, -t <val>

              Assume  a tree consisting of a single branch of specified length.  Default value is
              1.

       --tree, -T <tree.nh> Override --branch-length and use specified tree.

       --help, -h

              Display this help message and exit.