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.