leaf_renamer.py

Rename leaves in a phylogenetic tree to match the long names in the PhyloFisher database.

This utility is useful when you have a tree with Unique IDs as leaf names and want to replace them with the full taxonomic names from the database metadata for better readability and presentation.

leaf_renamer.py [OPTIONS] -d <database> -tr <tree> -o <output>

Required arguments:

• -d, --database <database> Path to PhyloFisher database directory
• -tr, --tree <input.tre> Path to input tree file in Newick format
• -o, --output <output.tre> Output tree file name

Optional arguments:

• -h, --help Show this help message and exit

Default leaf_renamer.py output:

• A tree file with leaf names replaced from Unique IDs to their corresponding long names from the database metadata.tsv file

NOTE: If multiple taxa in the database have the same long name, the Unique ID will be appended to the long name to maintain uniqueness (e.g., Homo_sapiens_Homosapi).