recipe phyml

Phylogenetic estimation using (Maximum) Likelihood

Homepage:

http://www.atgc-montpellier.fr/phyml/

Documentation:

https://github.com/stephaneguindon/phyml/blob/master/doc/phyml-manual.pdf

Developer docs:

https://github.com/stephaneguindon/phyml/

License:

GPL / GPL-3.0-only

Recipe:

/phyml/meta.yaml

Links:

biotools: phyml, doi: 10.1093/sysbio/syq010

PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. The main strength of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be processed. PhyML can process data sets made of multiple genes and fit sophisticated substitution models with heterogeneous components across partition elements.

package phyml

versions:

3.3.20220408-2,  3.3.20220408-1,  3.3.20220408-0,  3.3.20211231-2,  3.3.20211231-1,  3.3.20211231-0,  3.3.20200621-2,  3.3.20200621-1,  3.3.20200621-0, 

3.3.20220408-2,  3.3.20220408-1,  3.3.20220408-0,  3.3.20211231-2,  3.3.20211231-1,  3.3.20211231-0,  3.3.20200621-2,  3.3.20200621-1,  3.3.20200621-0,  3.3.20190909-1,  3.3.20190909-0,  3.3.20190908-0,  3.3.20190321-1,  3.3.20190321-0,  3.3.20180621-0,  3.3.20170530-0,  3.2.0-4,  3.2.0-3,  3.2.0-2,  3.2.0-0

depends libgcc-ng:

>=12

depends openmpi:

>=4.1.6,<5.0a0

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 phyml

and update with::

   mamba update phyml

To create a new environment, run:

mamba create --name myenvname phyml

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/phyml:<tag>

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

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