Source: https://github.com/aipoch/medical-research-skills

biopython-phylo

When to Use

• Converting phylogenetic tree files between Newick, NEXUS, and phyloXML formats.
• Traversing a tree to locate clades, prune taxa, or reroot at a specific node/outgroup.
• Computing pairwise distances, distance matrices, or basic tree statistics (e.g., branch length summaries).
• Producing quick tree visualizations as ASCII output for logs/CLI workflows.
• Generating publication-ready plots of trees using Matplotlib.

Key Features

• Read and write phylogenetic trees via Bio.Phylo with support for common formats (Newick/NEXUS/phyloXML).
• Tree manipulation utilities: traversal, clade selection, pruning, and rerooting.
• Distance computation and simple statistics derived from branch lengths/topology.
• Visualization options:
  • ASCII rendering for terminal output.
  • Matplotlib-based plotting for figures.