eggzilla/cmv

Visualize HMMs, CMs and their comparisons

cmv is a collection of tools for the visualisation of Hidden Markov Models (HMMV) and RNA-family models (CMV). Moreover it can visualise comparisons of these models (HMMCV,CMCV), and annotate linked regions in the structural alignments they were constructed from and via, 3rd party tools, in their consensus secondary structure.

They are available as a commandline tools and as a webservice cmvs.

The source code of cmv is open source and available via GitHub and Hackage (License GPL-3):

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For instruction how to use cmv please see the Help page.

Installation

For Linux we recommend installation via bioconda, for macOS usage of the docker container. The example input files used in the webservice (EGF, Piwi, Hammerhead Clan, tRNA Clan) can be retrieved here: Example input

Installation via bioconda - Linux

cmv can be installed with all dependencies via conda. Once you have conda installed simply type:

   conda install -c bioconda -c conda-forge cmv

Usage via biocontainer docker - MacOS

cmv can be retrieved and used as docker container with all dependencies via docker. Once you have docker installed simply type:

   docker run -i -t quay.io/biocontainers/cmv:1.0.8--0 /bin/bash

Installation via cabal-install

cmv is implemented in Haskell and can be installed via the Haskell package distribution sytem cabal. CMV is implemented in Haskell and can be installed via the Haskell package distribution sytem cabal. Additionally to cabal you require cairo, pango, happy and alex which can be installed via the distribution package manager e.g. Ubuntu:

    sudo apt-get install libcairo2 libpango1.0-0 libpangomm-1.4-dev happy alex

Once you have cabal installed simply type:

     cabal install cmv

Optional Dependencies:

cmv creates output which can be visualised via following optional dependencies.

• R2R
• forna

Precompiled Executables

• Linux (ghc-8.2.2) HMMV 1.0.8 x86_64
• Linux (ghc-8.2.2) HMMCV 1.0.8 x86_64
• Linux (ghc-8.2.2) CMV 1.0.8 x86_64
• Linux (ghc-8.2.2) CMCV 1.0.8 x86_64
• Linux (ghc-8.2.2) CMCV 1.0.8 x86_64

cmv's Issues

emission probabilities may not be in the correct order

Hi

I think the values of emission probabilities on MP states of a output pdf file does not match that of the .cm file.
In the attached cm file, the emission probabilities of state 30 is extracted as follows,
-3.167 -2.541 -3.627 1.624 -4.316 -2.747 0.395 -3.898 -3.644 3.055 -4.296 -0.329 0.071 -3.555 -1.803 -1.673
and the output pdf file is

It appears that CMV interprets the emission probs of the cm file as, from left to right, that of AA, AU, AG, AC, UU, ..., CU, CG.

However, In the infernal user's guide (p.102), the order of emission probabilities in a CM file is, from left to right, AA, AC, AG, AU, CA, CC, …, UG, UU.
I apologize if I have made a mistake, but I would appreciate it if you could check this. Thank you for your time.

RF00001.txt (please change .txt to .cm)
5S_rRNA.pdf

Add directedness to transitions

Thx @choener for reporting!

Link not working in description of code

http://www.gapjunction.eu/cmvs
This link is not working.