.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH HMM_VIEW "1" "May 2016" "hmm_view 1.4" "User Commands"
.SH NAME
hmm_view \- produces a graphical description of the state-transition
.SH 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)
.SH SYNOPSIS
hmm_view [OPTIONS] <hmm_fname> <cat_map_fname>|<cat_map_str>
.SH OPTIONS
.TP
\fB\-k\fR <nrcats>
Assume a separate version of each state for each of
<nrcats> rate categories.
.TP
\fB\-i\fR <icats>
Assume use of indel model for specified category names.
.TP
\fB\-t\fR <tree>
(Required with \fB\-i\fR) Tree topology to assume for indel
model (.nh file).
.TP
\fB\-C\fR <cats>
Show only the states corresponding to the specified
category names.
.TP
\fB\-R\fR <piv>
Reflect the HMM about the specified 'pivot' categories.
(Not yet implemented.)
.TP
\fB\-x\fR
Don't show unconnected states.