c. Module tree

The tree-module is used to de-branch and collapse phylogenetic trees. De-branching can be done based on distance and metadata. Branch-nodes with >2 leaf-nodes can be collapsed based on distance and can use metadata to avoid collapsing leaf-nodes that have different classifications. Disclaimer: the input tree below was generated using mash-tree, providing a rough phylogeny with limited accuracy.

De-branch and collapse based on distance

• De-branch tree based on distance:

tree.py --input test_genomes.dnd --debranch 0.05

• De-branch tree based on distance and collapse nodes:

tree.py --input test_genomes.dnd --debranch 0.05 --collapse

Phylogenetic trees showing the raw tree (left), the de-branched tree (middle), and collapsed tree (right)

De-branch and collapse based on metadata

In this example, metadata will be used to de-branch and collapse the tree. The accession nodes will be annotated using assign to help visualisation.

• Display the raw tree as family_genus_species_accession-number:

tree.py --input test_genomes.dnd | assign.py --input - --metadata_file metadata.tsv --columns "#family_#genus_#species_#accession"

• De-branch tree based on genus

tree.py --input test_genomes.dnd --metadata_file metadata.tsv --column genus | assign.py --input - --metadata_file metadata.tsv --columns "#family_#genus_#species_#accession"

• Collapse tree

tree.py --input test_genomes.dnd --metadata_file metadata.tsv --column genus --collapse | assign.py --input - --metadata_file metadata.tsv --columns "#family_#genus_#species_#accession"

Phylogenetic trees showing raw (left) and de-branched tree (right)

The final collapsed tree