bio-phylo-distance-calculations
Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use for creating distance matrices from alignments, building NJ/UPGMA trees, parsimony analysis, and generating bootstrap consensus trees.
npx skills add majiayu000/claude-skill-registry --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.
# Distance Calculations and Tree Building Compute distances from alignments and construct phylogenetic trees. ## Required Import ```python from Bio import Phylo, AlignIO from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor from Bio.Phylo.TreeConstruction import DistanceMatrix from Bio.Phylo.TreeConstruction import ParsimonyScorer, ParsimonyTreeConstructor, NNITreeSearcher from Bio.Phylo.Consensus import strict_consensus, majority_consensus, bootstrap_trees, bootstrap_consensus ``` ## Distance Matrix from Alignment ```python from Bio import AlignIO from Bio.Phylo.TreeConstruction import DistanceCalculator alignment = AlignIO.read('alignment.fasta', 'fasta') # Create calculator with distance model calculator = DistanceCalculator('identity') # Simple identity-based distance dm = calculator.get_distance(alignment) print(dm) # Available models for DNA calculator = DistanceCalculator('blastn') # BLASTN-style distance # Available models for protein calculator = DistanceCalculator('blosum62') # BLOSUM62-based distance ``` ## Available Distance Models | Model | Type | Description | |-------|------|-------------| | `identity` | DNA/Protein | 1 - (identical posit
- 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
- Consensus Tree Methods
- Tree Depths and Total Length
- Comparing Tree Distances
What does the bio-phylo-distance-calculations skill do?
Compute evolutionary distances and build phylogenetic trees using Biopython Bio.Phylo.TreeConstruction. Use for creating distance matrices from alignments, building NJ/UPGMA trees, parsimony analysis, and generating bootstrap consensus trees.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --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 majiayu000/claude-skill-registry, a repository with 534 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.