The cmv package

[ Tags: bioinformatics, gpl, library, program ] [ Propose Tags ]

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.


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Versions 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.0.6
Change log changelog
Dependencies aeson, base (>=4.5 && <5), BiobaseInfernal (==0.8.1.0), BiobaseTypes, BiobaseXNA, BioHMM (>=1.2.0), bytestring, cmdargs, cmv, colour, containers, diagrams-cairo, diagrams-core, diagrams-lib (>=1.4.1.2), directory, either-unwrap, filepath, mtl, parsec (>=3.1.9), ParsecTools, PrimitiveArray, StockholmAlignment (>=1.1.1), SVGFonts (>=1.6.0.2), template-haskell, text, vector [details]
License GPL-3
Author Florian Eggenhofer
Maintainer egg@informatik.uni-freiburg.de
Category Bioinformatics
Source repository head: git clone https://github.com/eggzilla/cmv
this: git clone https://github.com/eggzilla/cmv/tree/1.0.4(tag 1.0.4)
Uploaded Thu Sep 14 13:21:58 UTC 2017 by FlorianEggenhofer
Distributions NixOS:1.0.6
Executables HMMV, HMMCV, CMVJson, HMMCtoCMC, CMCtoHMMC, CMCWStoCMCV, CMV, CMCV
Downloads 215 total (33 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2017-09-14 [all 1 reports]
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Readme for cmv-1.0.4

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cmv

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):

  • GitHub Build Status Hackage Bioconda Docker Repository on Quay

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

Installation via bioconda

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

   conda install -c bioconda -c conda-forge cmv

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.

Precompiled Executables