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| HMM_VIEW(1) |
User Commands |
HMM_VIEW(1) |
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.
