- recipe pastml
Ancestral character reconstruction and visualisation for rooted phylogenetic trees.
- Homepage:
- Documentation:
- Developer docs:
- License:
GPL3 / GPL-3.0-or-later
- Recipe:
PastML provides fast methods for Ancestral Character Reconstruction (ACR) and visualisation on rooted phylogenetic trees. Given a rooted tree and its node annotations, it can either visualise them as-is, or infer ancestral node states based on the tip states, with a selection of maximum likelihood and parsimonious methods. The result is then visualised as a zoomable html map.
- package pastml¶
- versions:
1.9.43-0,1.9.40-0,1.9.39-0- depends biopython:
>=1.70- depends ete3:
>=3.1.1- depends itolapi:
>=4.0.0- depends jinja2:
>=2.11.0- depends numpy:
>=1.22- depends pandas:
>=1.0.0- depends python:
>=3.9- depends scipy:
>=1.5.0- 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 pastml and update with:: mamba update pastml
To create a new environment, run:
mamba create --name myenvname pastml
with
myenvnamebeing 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/pastml:<tag> (see `pastml/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/pastml/README.html)
