---
name: "hmm_view"
section: "1"
platform: "linux"
package: "phast"
version: "1.7+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/hmm_view"
---

# hmm\_view(1)

produces a graphical description of the state-transition

## 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.