alterlab-etetoolkit
De la autor
Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting tree files, doing phylogenomic comparative analysis, or producing publication tree graphics in Python. Part of the AlterLab Academic Skills suite.
Instalare
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-etetoolkit -a claude-code
Se instalează în .claude/skills/alterlab-etetoolkit/ · Fiecare comandă descarcă skill-ul direct de pe GitHub cu utilitarul open source skills.
Fără descărcare: licența acestui skill (GPL-3.0) nu ne permite să-i redistribuim fișierele. Comenzile de instalare le iau direct de pe GitHub.
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Verificări de siguranță pe SKILL.md
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De ce 75
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Skill-uri similare
Cele mai apropiate de acesta prin ce fac și când sunt folosite.
- etetoolkitK-Dense-AI/scientific-agent-skillsAnalyzes, manipulates, compares, annotates, and visualizes phylogenetic or other hierarchical trees with ETE 4. Supports Newick/Nexus tree I/O, topology edits and pattern matching, Robinson-Foulds comparisons, gene-tree evolutionary events and reconciliation, NCBI/GTDB taxonomy, SmartView exploration, and publication rendering. Applies to existing trees after alignment and phylogenetic inference, rather than inferring trees from raw sequences.Media★ 56K
- alterlab-phylogeneticsAlterLab-IEU/AlterLab-Academic-SkillsBuild phylogenetic trees end-to-end from raw sequences — MAFFT multiple sequence alignment, optional TrimAl trimming, IQ-TREE 3 maximum-likelihood inference with model selection and bootstraps, FastTree for large datasets, then visualize with ETE3 or FigTree. Use when reconstructing trees from sequences (FASTA) for evolutionary analysis, microbial genomics, viral phylodynamics, protein-family studies, or molecular-clock dating. For manipulating/comparing an EXISTING Newick tree (prune, root, Robinson-Foulds, duplication/speciation events) use alterlab-etetoolkit; for plain sequence parsing/translation use alterlab-biopython. Part of the AlterLab Academic Skills suite.Știință★ 84
- alterlab-neurokit2AlterLab-IEU/AlterLab-Academic-SkillsProcesses and analyzes physiological biosignals with the NeuroKit2 Python toolkit — ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements, or when computing heart rate variability (HRV), event-related potentials, complexity measures, autonomic nervous system assessment, or multi-modal physiological signal integration for psychophysiology research. Part of the AlterLab Academic Skills suite.Știință★ 84
- alterlab-matplotlibAlterLab-IEU/AlterLab-Academic-SkillsBuilds plots with the matplotlib Python library (pyplot and the object-oriented Figure/Axes API) for full low-level customization, exporting to PNG/PDF/SVG. Use when fine-grained control over individual plot elements is needed — custom line/scatter/bar/histogram/heatmap/contour/box/violin/3D plots, rcParams and style-sheet tuning, or GridSpec subplot layouts inside a scientific Python workflow. Does NOT cover opinionated journal-ready multi-panel figure workflows (Nature/Science/Cell formatting, colorblind-safe palettes, significance annotations); for those prefer alterlab-scientific-viz instead. Part of the AlterLab Academic Skills suite.Documente★ 84
- alterlab-biopythonAlterLab-IEU/AlterLab-Academic-SkillsManipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence files, automating BLAST, or fetching records from Entrez — for quick one-off database lookups use gget, for unified multi-service integration use bioservices. Part of the AlterLab Academic Skills suite.Date★ 84
- alterlab-edgartoolsAlterLab-IEU/AlterLab-Academic-SkillsAccesses, analyzes, and extracts data from SEC EDGAR filings using the edgartools Python library. Use when working with SEC filings, financial statements (income statement, balance sheet, cash flow), XBRL financial data, insider trading (Form 4), institutional holdings (13F), company financials, annual/quarterly reports (10-K, 10-Q), proxy statements (DEF 14A), 8-K current events, company screening by ticker/CIK/industry, multi-period financial analysis, or any SEC regulatory filings. Part of the AlterLab Academic Skills suite.Finanțe★ 84
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