alterlab-phylogenetics
De la autor
Build 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.
Instalare
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-phylogenetics -a claude-code
Se instalează în .claude/skills/alterlab-phylogenetics/ · Fiecare comandă descarcă skill-ul direct de pe GitHub cu utilitarul open source skills.
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De ce 77
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Skill-uri similare
Cele mai apropiate de acesta prin ce fac și când sunt folosite.
- alterlab-etetoolkitAlterLab-IEU/AlterLab-Academic-SkillsManipulate, 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.Documente★ 84
- phylogeneticsK-Dense-AI/scientific-agent-skillsBuilds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.Știință★ 56K
- 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-scikit-bioAlterLab-IEU/AlterLab-Academic-SkillsAnalyze biological data with scikit-bio — sequence analysis and alignments, phylogenetic trees, alpha/beta diversity metrics (including UniFrac), ordination (PCoA), PERMANOVA statistics, and FASTA/Newick I/O. Use for microbiome and community-ecology analysis — computing diversity, distance matrices, and ordination from feature tables. Part of the AlterLab Academic Skills suite.Știință★ 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-ggetAlterLab-IEU/AlterLab-Academic-SkillsRun fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanced BLAST use biopython, for multi-database Python workflows use bioservices. Part of the AlterLab Academic Skills suite.Date★ 84
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