Individual skill
biopython-phylo
Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required.
scientific-skills/Data Analysis/biopython-phylo/SKILL.md
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- bioinformatics Repository topic
- computational-biology Repository topic
- data-analysis Repository topic
- ai Repository topic
- biology Repository topic
- cancer-genomics Repository topic
- data-visualization Repository topic
- differential-expression Repository topic
- genomics Repository topic
- medical Repository topic
- data Derived category
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SKILL.mdcore · 7,013 bytesSKILL.mdcore · 7,013 bytesSKILL.mdcore · 7,013 bytesSKILL.mdcore · 7,013 bytesSKILL.mdcore · 7,013 bytesbiopython-phylo_audit_result_v1.jsonasset · 12,331 bytesconfig/task_config.jsonasset · 2 bytesreferences/phylogenetics.mddoc · 14,401 bytes
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> **Source**: [https://github.com/aipoch/medical-research-skills](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).