recipe veryfasttree

VeryFastTree -- speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies.

Homepage:

https://github.com/citiususc/veryfasttree

Documentation:

https://github.com/citiususc/veryfasttree/blob/v4.0.4/README.md

License:

GPL3 / GPL-3.0-only

Recipe:

/veryfasttree/meta.yaml

Links:

doi: 10.1093/bioinformatics/btaa582, doi: 10.1093/gigascience/giae055, biotools: veryfasttree

VeryFastTree is a highly-tuned implementation of the FastTree-2 tool that takes advantage of parallelization and vectorization strategies to speed up the inference of phylogenies for huge alignments.

package veryfasttree

versions:

4.0.4-1,  4.0.4-0,  4.0.03-0,  4.0.2-0,  4.0.1-0,  4.0-0,  3.2.1-2,  3.2.1-1,  3.2.1-0, 

4.0.4-1,  4.0.4-0,  4.0.03-0,  4.0.2-0,  4.0.1-0,  4.0-0,  3.2.1-2,  3.2.1-1,  3.2.1-0,  3.2.0-0,  3.1.1-1,  3.1.1-0,  3.1.0-1,  3.1.0-0,  3.0.1-0

depends _openmp_mutex:

>=4.5

depends libgcc:

>=13

depends libgomp:

depends libstdcxx:

>=13

requirements:

additional platforms:

linux-aarch64,  osx-arm64

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 veryfasttree

and update with::

   mamba update veryfasttree

To create a new environment, run:

mamba create --name myenvname veryfasttree

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 quay.io/biocontainers/veryfasttree:<tag>

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

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