recipe read2tree

Building phylogenetic trees directly from sequencing reads







doi: 10.1101/2022.04.18.488678

package read2tree

(downloads) docker_read2tree



depends biopython:

depends dendropy:

depends filelock:

depends iqtree:

depends lxml:

depends mafft:

depends natsort:

depends nextgenmap:

depends ngmlr:

depends numpy:

depends pyham:

depends pyparsing:

depends pysam:

depends python:

depends pyyaml:

depends requests:

depends samtools:

depends scipy:

depends tqdm:



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 read2tree

and update with::

   mamba update read2tree

To create a new environment, run:

mamba create --name myenvname read2tree

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 `read2tree/tags`_ for valid values for ``<tag>``)

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