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:

3.3.20220408-3,  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, 

3.3.20220408-3,  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:

• on libgcc >=13

• on openmpi >=4.1.6,<5.0a0

Additional platforms:

linux-aarch64

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install phyml

to add into an existing workspace instead, run:

pixi add phyml

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install phyml

Alternatively, to install into a new environment, run:

conda create -n envname phyml

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/phyml:<tag>

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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