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cmv: Detailed visualization of CMs, HMMs and their comparisions
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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Downloads
- cmv-1.0.8.tar.gz [browse] (Cabal source package)
- Package description (as included in the package)
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For package maintainers and hackage trustees
Candidates
| Versions [RSS] | 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.0.6, 1.0.7, 1.0.8 |
|---|---|
| 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 (>=1.1.2), SVGFonts (>=1.6.0.2), template-haskell, text, vector [details] |
| Tested with | ghc ==8.0.2, ghc ==8.2.2 |
| License | GPL-3.0-only |
| Author | Florian Eggenhofer |
| Maintainer | egg@informatik.uni-freiburg.de |
| Uploaded | by FlorianEggenhofer at 2018-01-28T20:19:04Z |
| Category | Bioinformatics |
| Source repo | head: git clone https://github.com/eggzilla/cmv this: git clone https://github.com/eggzilla/cmv/tree/1.0.8(tag 1.0.8) |
| Distributions | |
| Executables | HMMV, HMMCV, CMVJson, HMMCtoCMC, CMCtoHMMC, CMCWStoCMCV, CMV, CMCV |
| Downloads | 5343 total (27 in the last 30 days) |
| Rating | (no votes yet) [estimated by Bayesian average] |
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| Status | Docs available [build log] Last success reported on 2018-01-28 [all 1 reports] |
Readme for cmv-1.0.8
[back to package description]
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):
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:1.0.7--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.
Precompiled Executables
- Linux (ghc-8.2.2) HMMV 1.0.7 x86_64
- Linux (ghc-8.2.2) HMMCV 1.0.7 x86_64
- Linux (ghc-8.2.2) CMV 1.0.7 x86_64
- Linux (ghc-8.2.2) CMCV 1.0.7 x86_64
- Linux (ghc-8.2.2) CMCV 1.0.7 x86_64