bio-phylo-distance-calculations
Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use when creating distance matrices from alignments, building NJ/UPGMA trees, generating bootstrap consensus, or needing quick exploratory phylogenies before running full ML analysis.
npx skills add BioTender-max/awesome-bio-agent-skills --skill distance-calculations --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+, NCBI BLAST+ 2.15+ 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. # Distance Calculations and Tree Building **"Build a phylogenetic tree from my alignment"** → Compute evolutionary distance matrices from sequence alignments and construct neighbor-joining or UPGMA trees with bootstrap support. - Python: `Bio.Phylo.TreeConstruction.DistanceCalculator()`, `DistanceTreeConstructor()` Compute distances from alignments and construct phylogenetic trees. ## When to Use Distance Methods vs ML | Scenario | Recommended Method | |----------|-------------------| | Quick exploratory tree before committing to a long ML run | NJ | | Sanity check on data quality (unexpected groupings?) | NJ | | Very large datasets where ML is prohibitive | NJ | | Molecular clock data (ultrametric trees) | UPGMA (rare) | | Publication-quality trees | **ML (IQ-TREE2/RAxML-NG)**
- Version Compatibility
- When to Use Distance Methods vs ML
- Evolutionary Distance Corrections
- Required Import
- Distance Matrix from Alignment
- Available Distance Models
- Building Trees with Distance Methods
- Neighbor Joining (NJ)
- UPGMA
- One-Step Tree Building
- Pairwise Distances Between Taxa
- Creating Distance Matrix Manually
- Parsimony Tree Construction
- Bootstrap Analysis
What does the bio-phylo-distance-calculations skill do?
Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use when creating distance matrices from alignments, building NJ/UPGMA trees, generating bootstrap consensus, or needing quick exploratory phylogenies before running full ML analysis.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill distance-calculations --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.