Library
Biopython agent skills for Claude Code, Codex and other agents.
- skills
- 71
- Type
- Library
- Website
- biopython.org
- Official GitHub
- biopython
Biopython skills, ranked
Ranked by score. Sort bymost stars,trending,newest,recently updated
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. | GPTomics/ | 1.2k | 3 repos | ~4.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 2 | Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis. | aiming-lab/ | 15k | — | ~810 | Automated safety check: Pass | MIT | 1 mo ago |
| 3 | Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. | GPTomics/ | 1.2k | 3 repos | ~2.1k | Automated safety check: Pass | MIT | 1 mo ago |
| 4 | Primary Python toolkit for molecular biology. An agent skill from davila7/claude-code-templates. | davila7/ | 32k | 13 repos | ~3.4k | Automated safety check: Pass | MIT | today |
| 5 | 5.Gget CLI/Python toolkit for rapid bioinformatics queries. An agent skill from davila7/claude-code-templates. | davila7/ | 32k | 11 repos | ~6.3k | Automated safety check: Pass | MIT | today |
| 6 | Perform pairwise sequence alignment using Biopython Bio.Align.PairwiseAligner. | majiayu000/ | 666 | 4 repos | ~1.7k | Automated safety check: Pass | MIT | today |
| 7 | 7.Gget Queries 20+ bioinformatics resources through CLI/Python. An agent skill from K-Dense-AI/scientific-agent-skills. | K-Dense-AI/ | 48k | 1 repo | ~2.8k | Automated safety check: Notes | BSD-2-Clause | 2 days ago |
| 8 | Provides Biopython workflows for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). | K-Dense-AI/ | 48k | 1 repo | ~4.3k | Automated safety check: Notes | MIT | 2 days ago |
| 9 | Computational molecular biology library (sequence I/O, alignment, phylogenetics). | lamm-mit/ | 244 | — | ~3.9k | Automated safety check: Pass | Apache-2.0 | 1 mo ago |
| 10 | Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython, and write a Markdown report plus… | ClawBio/ | 1.2k | 1 repo | ~3.4k | Automated safety check: Pass | MIT | yesterday |
| 11 | Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. | wu-yc/ | 1.1k | 2 repos | ~4.2k | Automated safety check: Pass | No licence | 6 mo ago |
| 12 | Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic. | GPTomics/ | 1.2k | 2 repos | ~3.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 13 | Run remote BLAST searches against NCBI servers using Biopython Bio.Blast.NCBIWWW. | GPTomics/ | 1.2k | 2 repos | ~3.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 14 | Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). | GPTomics/ | 1.2k | 2 repos | ~3.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 15 | Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). | GPTomics/ | 1.2k | 2 repos | ~3.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 16 | Process multiple sequence files in batch using Biopython. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 17 | Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. | FreedomIntelligence/ | 3.1k | 1 repo | ~2k | Automated safety check: Pass | No licence | 2 mo ago |
| 18 | Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 19 | Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.5k | Automated safety check: Pass | No licence | 2 mo ago |
| 20 | Handle paired-end FASTQ files (R1/R2) using Biopython. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 21 | Perform geometric calculations on protein structures using Biopython Bio.PDB. | FreedomIntelligence/ | 3.1k | 1 repo | ~3.2k | Automated safety check: Pass | No licence | 2 mo ago |
| 22 | Parse and write protein structure files using Biopython Bio.PDB. | FreedomIntelligence/ | 3.1k | 1 repo | ~1.9k | Automated safety check: Pass | No licence | 2 mo ago |
| 23 | Modify protein structures using Biopython Bio.PDB. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.8k | Automated safety check: Pass | No licence | 2 mo ago |
| 24 | Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.3k | Automated safety check: Pass | No licence | 2 mo ago |
| 25 | Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. | FreedomIntelligence/ | 3.1k | 1 repo | ~2.6k | Automated safety check: Pass | No licence | 2 mo ago |
| 26 | Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. | GPTomics/ | 1.2k | 2 repos | ~8.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 27 | Parse and analyze multiple sequence alignments using Biopython. | majiayu000/ | 666 | 4 repos | ~5.5k | Automated safety check: Pass | MIT | today |
| 28 | Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk indexing using Biopython, pysam, or pyfastx. | GPTomics/ | 1.2k | 1 repo | ~3k | Automated safety check: Pass | MIT | 1 mo ago |
| 29 | Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CAI codon-optimized sequences. | GPTomics/ | 1.2k | 1 repo | ~3.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 30 | Read, write, and index compressed sequence files (gzip, bzip2, xz, BGZF) with Biopython and bgzip/samtools. | GPTomics/ | 1.2k | 1 repo | ~2.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 31 | Work with FASTQ quality scores using Biopython - access Phred scores, filter and trim by quality, compute per-position profiles, and convert between Sanger/Phred+33, Solexa, and Illumina/Phred+64… | GPTomics/ | 1.2k | 1 repo | ~3.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 32 | Filter and select sequences by criteria (length, ID, GC content, N content, motifs, patterns, description) using Biopython, streaming so large files never load into RAM. | GPTomics/ | 1.2k | 1 repo | ~3.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 33 | Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL, Stockholm) and re-encode FASTQ quality offsets using Biopython Bio.SeqIO. | GPTomics/ | 1.2k | 1 repo | ~2.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 34 | Find sequence motifs, degenerate IUPAC patterns, and transcription-factor binding sites in DNA/RNA using Biopython and regex, including position weight matrix (PWM/PSSM) scoring. | GPTomics/ | 1.2k | 1 repo | ~2.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 35 | Handle paired-end FASTQ files (R1/R2) using Biopython while keeping mates synchronized. | GPTomics/ | 1.2k | 1 repo | ~3.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 36 | Build model-corrected evolutionary distance matrices and distance trees (NJ, BIONJ, FastME, UPGMA) with Biopython Bio.Phylo plus R ape/phangorn/FastME. | GPTomics/ | 1.2k | 1 repo | ~4.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 37 | Read, write, and convert phylogenetic tree files with Biopython Bio.Phylo, and choose an annotation-preserving parser (treeio, DendroPy) when metadata matters. | GPTomics/ | 1.2k | 1 repo | ~3.7k | Automated safety check: Pass | MIT | 1 mo ago |
| 38 | Edit phylogenetic tree structure with Biopython Bio.Phylo, and treat rooting as a separate statistical inference rather than a display choice. | GPTomics/ | 1.2k | 1 repo | ~5k | Automated safety check: Pass | MIT | 1 mo ago |
| 39 | Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) with Biopython Bio.SeqIO, choosing between streaming, in-memory, and on-disk-indexed access. | GPTomics/ | 1.2k | 1 repo | ~3.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 40 | Select restriction enzymes for cloning or diagnostics using Biopython Bio.Restriction. | GPTomics/ | 1.2k | 1 repo | ~3.4k | Automated safety check: Pass | MIT | 1 mo ago |
| 41 | Predict restriction digest fragment sizes and gel patterns using Biopython Bio.Restriction. | GPTomics/ | 1.2k | 1 repo | ~2.6k | Automated safety check: Pass | MIT | 1 mo ago |
| 42 | Design and validate Type IIS scarless DNA assembly (Golden Gate, MoClo) using Biopython Bio.Restriction. | GPTomics/ | 1.2k | 1 repo | ~2.9k | Automated safety check: Pass | MIT | 1 mo ago |
| 43 | Build restriction maps showing enzyme cut positions and inter-site distances along DNA using Biopython Bio.Restriction. | GPTomics/ | 1.2k | 1 repo | ~2.3k | Automated safety check: Pass | MIT | 1 mo ago |
| 44 | Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. | GPTomics/ | 1.2k | 1 repo | ~2.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 45 | Generate reverse complements and complements of DNA/RNA sequences using Biopython, including IUPAC ambiguity codes, gapped alignments, and minus-strand features. | GPTomics/ | 1.2k | 1 repo | ~2.8k | Automated safety check: Pass | MIT | 1 mo ago |
| 46 | Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. | GPTomics/ | 1.2k | 1 repo | ~2.5k | Automated safety check: Pass | MIT | 1 mo ago |
| 47 | Calculate nucleotide and protein sequence properties (GC content, GC skew, molecular weight, melting temperature, isoelectric point, instability, hydropathy) with Biopython. | GPTomics/ | 1.2k | 1 repo | ~4k | Automated safety check: Pass | MIT | 1 mo ago |
| 48 | Slice, extract, and concatenate biological sequences and annotated records using Biopython. | GPTomics/ | 1.2k | 1 repo | ~2.7k | Automated safety check: Pass | MIT | 1 mo ago |
Questions, answered from the data.
What is the best Biopython skill?
Bio Alignment Io from GPTomics/bioSkills ranks first of the 71 Biopython skills listed here, with the highest score: its repository has 1.2k GitHub stars, 3 other GitHub owners carry a copy, its SKILL.md loads about 4.9k tokens and it passes the automated safety check with no findings. Next come Biopython Bioinformatics and Bio Write Sequences.
Is there an official Biopython skill?
None yet. All 71 Biopython skills listed here come from community repositories; a skill counts as official when the product's own GitHub organization publishes it.
How are these skills ranked?
By Skill Navigator score, which combines the GitHub stars of the skill's repository (shared across that repo's skills and discounted for large collections), how many other GitHub owners carry a copy of the skill, and automated SKILL.md quality checks, minus penalties for safety-check warnings and for each further skill from the same repository. Skills that fail the safety check are not listed.