PROGRAM: makeHKY

USAGE: makeHKY [OPTIONS] <kappa> > hky.mod

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.