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BI
bio-phylo-distance-calculations
Maintainer FreedomIntelligence · Last updated April 1, 2026
Compute pairwise phylogenetic distances and diversity metrics.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-phylo-distance-calculations
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Compute distances from alignments and construct phylogenetic trees.
- calculator = DistanceCalculator('identity') # Simple identity-based distance dm = calculator.get_distance(alignment) print(dm).
Source Doc
Excerpt From SKILL.md
Distance Matrix from Alignment
from Bio import AlignIO
from Bio.Phylo.TreeConstruction import DistanceCalculator
alignment = AlignIO.read('alignment.fasta', 'fasta')
## Available models for DNA
calculator = DistanceCalculator('blastn') # BLASTN-style distance
## Available models for protein
calculator = DistanceCalculator('blosum62') # BLOSUM62-based distance
Use cases
- Use bio-phylo-distance-calculations for genomics and bioinformatics workflows.
- Apply bio-phylo-distance-calculations to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- tree-io - Save constructed trees to files
- tree-visualization - Draw resulting trees
- tree-manipulation - Root and process built trees
- alignment/alignment-io - Read alignments for tree building
- alignment/msa-statistics - Alignment quality before tree building
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