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Found 12 Skills
Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RCV, treeness/RCV, parsimony informative sites, evolutionary rate, DVMC, tree length, alignment gap statistics, GC content, and bootstrap support using PhyKIT, Biopython, and DendroPy. Performs NJ/UPGMA/parsimony tree construction, Robinson-Foulds distance, Mann-Whitney U tests, and batch analysis across gene families. Integrates with ToolUniverse for sequence retrieval (NCBI, UniProt, Ensembl) and tree annotation. Use when processing FASTA/PHYLIP/Nexus/Newick files, computing phylogenetic metrics, comparing taxa groups, or answering questions about alignments, trees, parsimony, or molecular evolution.
Comprehensive guide for MDAnalysis - the Python library for analyzing molecular dynamics trajectories. Use for trajectory loading, RMSD/RMSF calculations, distance/angle/dihedral analysis, atom selections, hydrogen bonds, solvent accessible surface area, protein structure analysis, membrane analysis, and integration with Biopython. Essential for MD simulation analysis.
Comprehensive guide for Biopython - the premier Python library for computational biology and bioinformatics. Use for DNA/RNA/protein sequence analysis, file I/O (FASTA, FASTQ, GenBank, PDB), sequence alignment, BLAST searches, phylogenetic analysis, structure analysis, and NCBI database access.
NCBI BLAST sequence similarity search using BioPython. Use when a user wants to run BLAST programmatically with blastn/blastp and retrieve results in JSON format.
CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID mapping across services. For quick single-database lookups use gget; for sequence/file manipulation use biopython.
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
Use when "scientific computing", "astronomy", "astropy", "bioinformatics", "biopython", "symbolic math", "sympy", "statistics", "statsmodels", "scientific Python"
Expert-level biology, biotechnology, genetics, bioinformatics, and computational biology
Read/write FASTA, GenBank, FASTQ files. Sequence manipulation (complement, translate). Indexed random access via faidx. For NGS pipelines (SAM/BAM/VCF), use pysam. For BLAST, use gget or blat-integration.