Supertree Module

Rule create_astral_input[source]

Concatenate single-gene trees into one file.


Rule astral[source]

Use ASTRAL to infer a coalescence-based tree.

Conda
name: astral
channels:
  - bioconda
dependencies:
  - astral-tree=5.7.8-0

Rule supertree_ascii[source]

Displays the supertree in ASCII format.

Conda
channels:
  - conda-forge
dependencies:
  - coreutils
  - python=3.9
  - pip
  - pip:
    - phykit==1.17.0

Rule supertree_render[source]

Renders the supertree in SVG and PNG formats.

Conda
channels:
  - conda-forge
dependencies:
  - ghostscript=9.54.0
  - typer
  - python=3.9
  - pip
  - pip:
    - numpy==1.22.4
    - toytree==2.0.1