Gene Tree Module

Rule gene_tree_iqtree[source]

Use IQTREE on the gene alignments.

Conda

name: iqtree
channels:
  - bioconda
  - conda-forge
dependencies:
  - libzlib=1.2.12
  - iqtree=2.2.0.3

Rule gene_tree_ascii[source]

Displays the gene tree in ASCII format.

Conda

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

Rule gene_tree_render[source]

Renders the gene tree 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

Rule gene_tree_consensus_render[source]

Renders the consensus gene tree tree 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