scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
72
70%
Does it follow best practices?
Impact
63%
2.86xAverage score across 3 eval scenarios
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The risk profile of this skill
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tessl review fix ./skills/bio/scikit-bio/SKILL.mdEvaluation results
88%
68%Comparative Phylogenetic Analysis of Bacterial Isolates
Phylogenetic tree construction methods
nj() for neighbor joining
0%
100%
upgma() for UPGMA
0%
100%
GME/BME scalability note
0%
100%
DistanceMatrix class
0%
100%
Patristic distances
50%
50%
Cophenetic matrix
0%
62%
Robinson-Foulds distance
33%
66%
PCoA on distance matrix
30%
100%
Newick output
100%
100%
uv install command
0%
100%
36%
30%Gene Characterization: Alignment and Translation Pipeline
Sequence class selection and alignment methods
DNA class usage
0%
100%
RNA class for transcription
0%
100%
Protein class for translation
0%
100%
FASTQ quality via positional_metadata
0%
20%
local_pairwise_align_ssw for DNA
0%
0%
StripedSmithWaterman for protein
0%
0%
Affine gap penalties
60%
0%
Degap before realignment
0%
0%
Generator-based FASTQ reading
0%
0%
uv install command
0%
100%
65%
22%Gut Microbiome Diversity Analysis: Healthy vs IBD Patients
Diversity analysis best practices
Integer counts
100%
100%
Faith's PD tree param
50%
70%
UniFrac tree param
0%
0%
PERMANOVA permutations
0%
100%
PERMDISP alongside PERMANOVA
0%
0%
PCoA on distance matrix
100%
100%
partial_beta_diversity for pairs
0%
0%
Alpha result as Series
100%
100%
Beta result as DistanceMatrix
100%
100%
uv install command
0%
100%
Permutation test 999+
100%
100%
- Repository
- wu-yc/LabClaw
- Commit
df37802
- Evaluated
- Agent
- Claude Code
- Model
- Claude Sonnet 4.6
Table of Contents
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