NAME

       hmm_view - produces a graphical description of the state-transition

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)

SYNOPSIS

       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.