- recipe phame
A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, and full genomes.
- Homepage:
- License:
GPLV2
- Recipe:
- Links:
biotools: phame
- package phame¶
- versions:
1.0.3-1,1.0.3-0,1.0.2-0,1.0.1-0,1.0.0-1,1.0-0- depends bbmap:
>=37.62- depends bcftools:
>=1.7- depends bowtie2:
>=2.3.4.1- depends bwa:
>=0.7.12- depends cmake:
>=3.0.1- depends curl:
>=7.60.0- depends fasttree:
>=2.1.9- depends hyphy:
>=2.3.12- depends iqtree:
>=1.6.7- depends mafft:
>=7.313- depends mummer:
>=3.23- depends muscle:
>=3.8.31- depends openmpi:
>=3.1.0- depends paml:
>=4.9- depends perl:
- depends perl-app-cpanminus:
>=1.7039- depends perl-bioperl:
>=1.7.2- depends perl-file-path:
>=2.12- depends perl-getopt-long:
>=2.50- depends perl-io-handle:
>=1.28- depends perl-io-handle:
>=1.35- depends perl-parallel-forkmanager:
>=1.17- depends perl-statistics-distributions:
>=1.02- depends raxml:
>=8.2.10- depends samtools:
>=1.7- requirements:
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 phame and update with:: mamba update phame
To create a new environment, run:
mamba create --name myenvname phame
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/phame:<tag> (see `phame/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/phame/README.html)
