Supermatrix Module

Rule concatenate_alignments[source]

Concatenate alignments into a single supermatrix.

https://jlsteenwyk.com/PhyKIT/usage/index.html#create-concatenation-matrix

Conda

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

Rule supermatrix_alignment_summary[source]

Summarizes the supermatrix alignment using BioKIT

https://jlsteenwyk.com/BioKIT/usage/index.html#alignment-summary https://jlsteenwyk.com/tutorials/phylogenomics_made_easy.html

Conda

channels:
  - conda-forge
dependencies:
  - coreutils
  - python=3.9
  - pip
  - pip:
    - git+https://github.com/JLSteenwyk/BioKIT.git

Rule supermatrix_iqtree[source]

Use IQTREE on the supermatrix.

Conda

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

Rule supermatrix_ascii[source]

Displays the tree in ASCII format.

Conda

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

Rule supermatrix_tree_render[source]

Renders the supermatrix 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 supermatrix_consensus_tree_render[source]

Renders the consensus supermatrix 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