- recipe alloshp
From mapped reads to Single Homeologous Polymorphisms (SHPs): pipeline for phylogenetic studies of allopolyploids
- Homepage:
- License:
APACHE / Apache-2.0
- Recipe:
- Links:
This 3-step protocol computes Whole Genome Alignments (WGA) to discover Single Homeologous Polymorphisms (SHPs) out of reads mapped to concatenated genome sequeces. It requires FASTA and VCF input files and produces multiple sequence alignments of subgenomes that make up allopolyploids.
- package alloshp¶
- Versions:
2025.09.12-0,2025.09.08-0,2025.09.08d-0- Depends:
on bzip2
on coreutils
on gnuplot
on grep
on gsalign
on gzip
on libgcc
>=13on make
on perl
on perl-db_file
on red
- 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 alloshp
to add into an existing workspace instead, run:
pixi add alloshp
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 alloshp
Alternatively, to install into a new environment, run:
conda create -n envname alloshp
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/alloshp:<tag>
(see alloshp/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/alloshp/README.html)
