bio-phylo-tree-io
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, or handling multiple trees.
npx skills add BioTender-max/awesome-bio-agent-skills --skill tree-io --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Tree I/O **"Read and convert my phylogenetic tree files"** → Parse trees from Newick, Nexus, PhyloXML, or NeXML formats and convert between formats for use in different tools. - Python: `Bio.Phylo.read('tree.nwk', 'newick')`, `Bio.Phylo.convert()` Parse, write, and convert phylogenetic tree files in various formats. ## Required Import ```python from Bio import Phylo from io import StringIO ``` ## Supported Formats | Format | Extension | Description | |--------|-----------|-------------| | `newick` | .nwk, .tre, .tree | Standard format with branch lengths | | `nexus` | .nex, .nxs | Rich format with annotations (PAUP, MrBayes) | | `phyloxml` | .xml | XML format with metadata support | | `nexml` | .nexml | Modern XML format | | `cdao` | .rdf | RDF format (limited use) | ## Reading Trees ```python
- Version Compatibility
- Required Import
- Supported Formats
- Reading Trees
- Writing Trees
- Serialize to String
- Format Conversion
- Quick Tree Inspection
- Accessing Tree Structure
- Tree from Newick String Patterns
- Working with PhyloXML Metadata
- Handling Multiple Trees
- Iterating Over Large Tree Files
- Common Newick Format Variations
What does the bio-phylo-tree-io skill do?
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use when parsing Newick, Nexus, PhyloXML, or NeXML tree formats, converting between formats, or handling multiple trees.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill tree-io --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.