PROGRAM: hmm_view

DESCRIPTION: produces a graphical description of the state-transition
structure of a phylo-HMM, which can be converted to a viewable image
using the 'dot' program. (http://www.graphviz.org)

USAGE: hmm_view [OPTIONS] <hmm_fname> <cat_map_fname>|<cat_map_str>

OPTIONS:
    -k <nrcats>   Assume a separate version of each state for each of 
                  <nrcats> rate categories. 
    -i <icats>    Assume use of indel model for specified category names.
    -t <tree>     (Required with -i) Tree topology to assume for indel
                  model (.nh file).
    -C <cats>     Show only the states corresponding to the specified
                  category names.
    -R <piv>      Reflect the HMM about the specified 'pivot' categories.
                  (Not yet implemented.)
    -x            Don't show unconnected states.