recipe bioconductor-fastreer

Phylogenetic, Distance and Other Calculations on VCF and Fasta Files






Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on the VCF or FASTA file for fast execution.

package bioconductor-fastreer

(downloads) docker_bioconductor-fastreer



depends openjdk:

depends r-ape:

depends r-base:


depends r-data.table:

depends r-dynamictreecut:

depends r-r.utils:

depends r-rjava:

depends r-stringr:



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 bioconductor-fastreer

and update with::

   mamba update bioconductor-fastreer

To create a new environment, run:

mamba create --name myenvname bioconductor-fastreer

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 `bioconductor-fastreer/tags`_ for valid values for ``<tag>``)

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