- recipe r-ggmsa
Supports visualizing multiple sequence alignment of DNA and protein sequences using 'ggplot2'. It supports a number of colour schemes, including Chemistry, Clustal, Shapely, Taylor and Zappo. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as aligning a phylogenetic tree produced by 'ggtree' with multiple sequence alignment.
- Homepage:
- License:
OTHER / Artistic-2.0
- Recipe:
- package r-ggmsa¶
- Versions:
1.0.2-4,1.0.2-3,1.0.2-2,1.0.2-1,1.0.2-0- Depends:
on bioconductor-biostrings
on bioconductor-r4rna
on r-aplot
on r-base
>=4.4,<4.5.0a0on r-dplyr
on r-ggalt
on r-ggforce
on r-ggplot2
on r-magrittr
on r-rcolorbrewer
on r-seqmagick
on r-stringr
on r-tidyr
- 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 r-ggmsa
to add into an existing workspace instead, run:
pixi add r-ggmsa
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 r-ggmsa
Alternatively, to install into a new environment, run:
conda create -n envname r-ggmsa
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/r-ggmsa:<tag>
(see r-ggmsa/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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/r-ggmsa/README.html)
