- recipe phyml
Phylogenetic estimation using (Maximum) Likelihood
- Homepage:
- Documentation:
https://github.com/stephaneguindon/phyml/blob/master/doc/phyml-manual.pdf
- Developer docs:
- License:
GPL / GPL-3.0-only
- Recipe:
- 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:
- additional platforms:
linux-aarch64
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>``)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
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