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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Properties

Versions 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5
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-lib (>=1.3.1.0), directory, either-unwrap, filepath, mtl, parsec (>=3.1.9), ParsecTools, PrimitiveArray, StockholmAlignment (>=1.1.1), SVGFonts (>=1.6), 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/1.0.2(tag 1.0.2)
Uploaded Thu Jun 22 13:25:01 UTC 2017 by FlorianEggenhofer
Distributions NixOS:1.0.3
Executables HMMV, HMMCV, CMVJson, HMMCtoCMC, CMCtoHMMC, CMCWStoCMCV, CMV, CMCV
Downloads 129 total (40 in the last 30 days)
Rating 0.0 (0 ratings) [clear rating]
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Status Docs available [build log]
Last success reported on 2017-06-22 [all 1 reports]
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Readme for cmv-1.0.2

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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

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

Optional Dependencies:

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

Installation via bioconda

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

   conda install -c bioconda cmv=1.0.0 

Installation via cabal-install

cmv is implemented in Haskell and can be installed via the Haskell package distribution sytem cabal. Once you have cabal installed simply type:

     cabal install cmv

Precompiled Executables