recipe phame

A tool to derive SNP matrices and phylogenetic tree from raw reads, contigs, and full genomes.







biotools: phame

package phame

(downloads) docker_phame



depends bbmap:


depends bcftools:


depends bowtie2:


depends bwa:


depends cmake:


depends curl:


depends fasttree:


depends hyphy:


depends iqtree:


depends mafft:


depends mummer:


depends muscle:


depends openmpi:


depends paml:


depends perl:

depends perl-app-cpanminus:


depends perl-bioperl:


depends perl-file-path:


depends perl-getopt-long:


depends perl-io-handle:


depends perl-io-handle:


depends perl-parallel-forkmanager:


depends perl-statistics-distributions:


depends raxml:


depends samtools:




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 myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `phame/tags`_ for valid values for ``<tag>``)

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