- recipe metaphlan
Metagenomic Phylogenetic Analysis.
- Homepage:
- Documentation:
- License:
MIT / MIT
- Recipe:
- Links:
doi: 10.1038/nmeth.2066, biotools: metaphlan, usegalaxy-eu: metaphlan
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data with species level resolution. From version 2.0 MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.
- package metaphlan¶
- versions:
4.2.2-0,4.2.1-0,4.2.0-0,4.1.1-0,4.1.0-0,4.0.6-0,4.0.5-0,4.0.4-0,4.0.3-0,4.2.2-0,4.2.1-0,4.2.0-0,4.1.1-0,4.1.0-0,4.0.6-0,4.0.5-0,4.0.4-0,4.0.3-0,4.0.2-0,4.0.1-0,4.0.0-0,3.1.0-0,3.0.14-0,3.0.13-0,3.0.12-0,3.0.11-0,3.0.10-0,3.0.9-0,3.0.8-0,3.0.7-2,3.0.7-1,3.0.7-0,3.0.6-0,3.0.5-0,3.0.4-1,3.0.4-0,3.0.3-0,3.0.2-0,3.0.1-0,3.0-4,3.0-3,3.0-2,3.0-1,3.0-0,3.0.0.alpha-1,3.0.0.alpha-0,2.8.1-1,2.8.1-0- depends bioconductor-microbiome:
- depends biom-format:
- depends biopython:
- depends blast:
- depends bowtie2:
>=2.3.0- depends cmseq:
- depends dendropy:
- depends h5py:
- depends hclust2:
- depends matplotlib-base:
- depends minimap2:
>=2.26- depends muscle:
>=3.8.1551- depends numpy:
- depends pandas:
- depends phylophlan:
- depends pysam:
- depends python:
>=3.7- depends r-ape:
- depends r-base:
>=4- depends r-biocmanager:
- depends r-compositions:
- depends r-essentials:
- depends r-optparse:
- depends r-rbiom:
- depends raxml:
>=8.2.10- depends requests:
- depends samtools:
- depends scipy:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install metaphlan and update with:: mamba update metaphlan
To create a new environment, run:
mamba create --name myenvname metaphlan
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/metaphlan:<tag> (see `metaphlan/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/metaphlan/README.html)
