- recipe quasirecomb
Software of Inference of Quasispecies subjected to Recombination
- Homepage:
- License:
GPL3 / GNU GPLv3
- Recipe:
- Links:
biotools: QuasiRecomb, doi: 10.1089/cmb.2012.0232
QuasiRecomb presents a jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. It offers an implementation of the EM algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies.
- package quasirecomb¶
- Versions:
1.2-1,1.2-0- Depends:
on openjdk
>=8on python
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install quasirecomb
to add into an existing workspace instead, run:
pixi add quasirecomb
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install quasirecomb
Alternatively, to install into a new environment, run:
conda create -n envname quasirecomb
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/quasirecomb:<tag>
(see quasirecomb/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Notes¶
QuasiRecomb is a Java program that comes with a custom wrapper shell script.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/quasirecomb/README.html)
