Quality control module¶

This module contains several rules for ensuring quality control of the aligned sequences, most notably via construction of a maximum likelihood tree and the use of the phytest package.

Rules¶

Rule tree[source]¶

Use iqtree to generate the maximum likelihood phylogenomic tree.

Input¶:

the aligned fasta file from the align rule

Output¶:

the files output by iqtree, most notably *.treefile

Config¶:

• tree.iqtree2 –

  the iqtree config parameters passed on the command line

  default: ['-nt AUTO', '-m HKY+G', '-bb 1000', '-seed 847202098']

  Note: -pre is set automatically by McCoy. -seed will also be take on the value of the environment variable IQTREE_SEED if set.

• tree.threads – the maximum number of threads available to iqtree

  default: 10

• tree.resources – the resources to request when submitting this rule to a cluster

  default: {'runtime': 20, 'mem_mb': 16000}

Conda¶:

channels:
  - bioconda
dependencies:
  - iqtree==2.1.2

Rule render_mltree[source]¶

Renders the maximum likelihood tree from iqtree in SVG and HTML format.

Input¶:

the tree file produced by the tree rule

Output¶:

• svg – the maximum likeihood tree (svg)

• html – the maximum likeihood tree (html)

Conda¶:

channels:
  - conda-forge
dependencies:
  - toytree=2.0.5
  - typer
  - pip:
    - numpy==1.22.4

Rule render_consensus_mltree[source]¶

Renders the consensus maximum likelihood tree from iqtree in SVG and HTML format.

Conda¶:

channels:
  - conda-forge
dependencies:
  - toytree=2.0.5
  - typer
  - pip:
    - numpy==1.22.4