[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6DAVCRDDK74H4XTYZ74DVSH":3,"skill-same:01M6DAVCRDDK74H4XTYZ74DVSH":100},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":18,"publishedAt":39,"linkOnly":40,"markdownContent":41,"markdownBody":42,"frontMatter":43,"refName":44,"commitSha":45,"skillDirectory":46,"forksCount":14,"repositoryHtmlUrl":47,"repositoryHomepageUrl":6,"ownerHtmlUrl":48,"ownerBlogUrl":6,"ownerDescription":6,"updatedAt":49,"install":50,"resources":63},"01M6DAVCRDDK74H4XTYZ74DVSH","tooluniverse-phylogenetics",null,"Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RCV, treeness\u002FRCV, parsimony informative sites, evolutionary rate, DVMC, tree length, alignment gap statistics, GC content, and bootstrap support using PhyKIT, Biopython, and DendroPy. Performs NJ\u002FUPGMA\u002Fparsimony 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\u002FPHYLIP\u002FNexus\u002FNewick files, computing phylogenetic metrics, comparing taxa groups, or answering questions about alignments, trees, parsimony, or molecular evolution.","Prekzursil\u002Fagent-skills-toolchain","Prekzursil","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F54636077?v=4","01M6DACZ1PCQHD99SCR1YXG28B","Andrei Mihai Visalon","01M6DACZ670WZF535V3WYYSS4Z",0,"MIT","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002F.agents\u002Flibrary\u002Fskills\u002Ftooluniverse-phylogenetics\u002FSKILL.md",[],[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],"tooluniverse phylogenetics","phylogenetics","Nexus","gap","tests","molecular","statistics","across","files","alignment","support","gc","ready","use","evolution","analysis","biopython","Production","batch","bootstrap","2026-11-10 10:12:30",false,"---\nname: tooluniverse-phylogenetics\ndescription: Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics. Computes treeness, RCV, treeness\u002FRCV, parsimony informative sites, evolutionary rate, DVMC, tree length, alignment gap statistics, GC content, and bootstrap support using PhyKIT, Biopython, and DendroPy. Performs NJ\u002FUPGMA\u002Fparsimony 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\u002FPHYLIP\u002FNexus\u002FNewick files, computing phylogenetic metrics, comparing taxa groups, or answering questions about alignments, trees, parsimony, or molecular evolution.\n---\n\n# Phylogenetics and Sequence Analysis\n\nPhyKIT, Biopython, and DendroPy for alignment\u002Ftree analysis, evolutionary metrics, and comparative genomics.\n\n## LOOK UP, DON'T GUESS\nWhen uncertain about any scientific fact, SEARCH databases first.\n\n---\n\n## When to Use\n\nFASTA\u002FPHYLIP\u002FNexus\u002FNewick files; treeness, RCV, DVMC, evolutionary rate, parsimony sites, tree length, bootstrap; group comparisons (Mann-Whitney U); tree construction (NJ\u002FUPGMA\u002Fparsimony); Robinson-Foulds distance.\n\n**BixBench**: 33 questions across bix-4, bix-11, bix-12, bix-25, bix-35, bix-38, bix-45, bix-60.\n\n**NOT for**: MSA generation (MUSCLE\u002FMAFFT), ML trees (IQ-TREE\u002FRAxML), Bayesian (MrBayes\u002FBEAST).\n\n---\n\n## Required Packages\n\n```python\nimport numpy as np, pandas as pd\nfrom scipy import stats\nfrom Bio import AlignIO, Phylo, SeqIO\nfrom phykit.services.tree.treeness import Treeness\nfrom phykit.services.tree.total_tree_length import TotalTreeLength\nfrom phykit.services.tree.evolutionary_rate import EvolutionaryRate\nfrom phykit.services.tree.dvmc import DVMC\nfrom phykit.services.tree.treeness_over_rcv import TreenessOverRCV\nfrom phykit.services.alignment.parsimony_informative_sites import ParsimonyInformative\nfrom phykit.services.alignment.rcv import RelativeCompositionVariability\nimport dendropy\n```\n\n---\n\n## Workflow Decision Tree\n\n```\nALIGNMENT ANALYSIS (FASTA\u002FPHYLIP):\n  Parsimony sites → phykit_parsimony_informative()\n  RCV → phykit_rcv()\n  Gap % → alignment_gap_percentage()\n\nTREE ANALYSIS (Newick):\n  Treeness → phykit_treeness()\n  Tree length → phykit_tree_length()\n  Evolutionary rate → phykit_evolutionary_rate()\n  DVMC → phykit_dvmc()\n  Bootstrap → extract_bootstrap_support()\n\nCOMBINED: Treeness\u002FRCV → phykit_treeness_over_rcv(tree, aln)\n\nTREE CONSTRUCTION: NJ → build_nj_tree(); UPGMA → build_upgma_tree(); Parsimony → build_parsimony_tree()\n\nGROUP COMPARISON: batch metrics → Mann-Whitney U → summary stats\n\nTREE COMPARISON: Robinson-Foulds → robinson_foulds_distance()\n```\n\n---\n\n## Quick Reference\n\n| Metric | Input | Description |\n|--------|-------|-------------|\n| Treeness | Newick | Internal \u002F total branch length |\n| RCV | FASTA\u002FPHYLIP | Relative Composition Variability |\n| Treeness\u002FRCV | Both | Signal quality ratio |\n| Tree Length | Newick | Sum of all branch lengths |\n| Evolutionary Rate | Newick | Total length \u002F num terminals |\n| DVMC | Newick | Degree of Violation of Molecular Clock |\n| Parsimony Sites | FASTA\u002FPHYLIP | Sites with >=2 chars appearing >=2 times |\n\n---\n\n## Common Patterns\n\n### Single Metric Across Groups\n```python\nfungi_dvmc = batch_dvmc(discover_gene_files(\"data\u002Ffungi\"))\nanimal_dvmc = batch_dvmc(discover_gene_files(\"data\u002Fanimals\"))\nprint(f\"Fungi median: {np.median(list(fungi_dvmc.values())):.4f}\")\n```\n\n### Statistical Comparison\n```python\nu_stat, p_value = stats.mannwhitneyu(list(g1.values()), list(g2.values()), alternative='two-sided')\n```\n\n### Filtering + Metric\nFilter by gap percentage \u003C 5%, then compute treeness\u002FRCV on filtered set.\n\n### Batch Processing\n```python\ngene_files = discover_gene_files(\"data\u002F\")  # → [{gene_id, aln_file, tree_file}]\ntreeness_results = batch_treeness(gene_files)  # → {gene_id: value}\n```\n\n---\n\n## Answer Extraction\n\n| Pattern | Method |\n|---------|--------|\n| \"median X\" | `np.median(values)` |\n| \"maximum X\" | `np.max(values)` |\n| \"difference in median\" | `abs(np.median(a) - np.median(b))` |\n| \"Mann-Whitney U\" | `stats.mannwhitneyu(a, b)[0]` |\n| \"fold-change\" | `np.median(a) \u002F np.median(b)` |\n\n**Rounding**: PhyKIT default 4 decimals. U stats = integer. Question wording overrides.\n\n---\n\n## Interpretation\n\n| Metric | Good | Acceptable | Poor |\n|--------|------|-----------|------|\n| Treeness | >0.8 | 0.5-0.8 | \u003C0.5 |\n| RCV | \u003C0.2 | 0.2-0.5 | >0.5 |\n| Treeness\u002FRCV | >2.0 | 1.0-2.0 | \u003C1.0 |\n| Bootstrap | >95% | 70-95% | \u003C70% |\n| Parsimony sites | >30% | 10-30% | \u003C10% |\n\n## Completeness Checklist\n\nAll files identified; group structure detected; correct PhyKIT function; ALL genes processed (not sample); correct test; 4-decimal rounding; specific statistic (median\u002Fmax\u002FU\u002Fp); Mann-Whitney `alternative='two-sided'`.\n\n---\n\n## References\n\n`references\u002Fsequence_alignment.md`, `references\u002Ftree_building.md`, `references\u002Fparsimony_analysis.md`, `scripts\u002Ftree_statistics.py`\n- PhyKIT: https:\u002F\u002Fjlsteenwyk.com\u002FPhyKIT\u002F\n- Biopython Phylo: https:\u002F\u002Fbiopython.org\u002Fwiki\u002FPhylo\n- DendroPy: https:\u002F\u002Fdendropy.org\u002F\n","# Phylogenetics and Sequence Analysis\n\nPhyKIT, Biopython, and DendroPy for alignment\u002Ftree analysis, evolutionary metrics, and comparative genomics.\n\n## LOOK UP, DON'T GUESS\nWhen uncertain about any scientific fact, SEARCH databases first.\n\n---\n\n## When to Use\n\nFASTA\u002FPHYLIP\u002FNexus\u002FNewick files; treeness, RCV, DVMC, evolutionary rate, parsimony sites, tree length, bootstrap; group comparisons (Mann-Whitney U); tree construction (NJ\u002FUPGMA\u002Fparsimony); Robinson-Foulds distance.\n\n**BixBench**: 33 questions across bix-4, bix-11, bix-12, bix-25, bix-35, bix-38, bix-45, bix-60.\n\n**NOT for**: MSA generation (MUSCLE\u002FMAFFT), ML trees (IQ-TREE\u002FRAxML), Bayesian (MrBayes\u002FBEAST).\n\n---\n\n## Required Packages\n\n```python\nimport numpy as np, pandas as pd\nfrom scipy import stats\nfrom Bio import AlignIO, Phylo, SeqIO\nfrom phykit.services.tree.treeness import Treeness\nfrom phykit.services.tree.total_tree_length import TotalTreeLength\nfrom phykit.services.tree.evolutionary_rate import EvolutionaryRate\nfrom phykit.services.tree.dvmc import DVMC\nfrom phykit.services.tree.treeness_over_rcv import TreenessOverRCV\nfrom phykit.services.alignment.parsimony_informative_sites import ParsimonyInformative\nfrom phykit.services.alignment.rcv import RelativeCompositionVariability\nimport dendropy\n```\n\n---\n\n## Workflow Decision Tree\n\n```\nALIGNMENT ANALYSIS (FASTA\u002FPHYLIP):\n  Parsimony sites → phykit_parsimony_informative()\n  RCV → phykit_rcv()\n  Gap % → alignment_gap_percentage()\n\nTREE ANALYSIS (Newick):\n  Treeness → phykit_treeness()\n  Tree length → phykit_tree_length()\n  Evolutionary rate → phykit_evolutionary_rate()\n  DVMC → phykit_dvmc()\n  Bootstrap → extract_bootstrap_support()\n\nCOMBINED: Treeness\u002FRCV → phykit_treeness_over_rcv(tree, aln)\n\nTREE CONSTRUCTION: NJ → build_nj_tree(); UPGMA → build_upgma_tree(); Parsimony → build_parsimony_tree()\n\nGROUP COMPARISON: batch metrics → Mann-Whitney U → summary stats\n\nTREE COMPARISON: Robinson-Foulds → robinson_foulds_distance()\n```\n\n---\n\n## Quick Reference\n\n| Metric | Input | Description |\n|--------|-------|-------------|\n| Treeness | Newick | Internal \u002F total branch length |\n| RCV | FASTA\u002FPHYLIP | Relative Composition Variability |\n| Treeness\u002FRCV | Both | Signal quality ratio |\n| Tree Length | Newick | Sum of all branch lengths |\n| Evolutionary Rate | Newick | Total length \u002F num terminals |\n| DVMC | Newick | Degree of Violation of Molecular Clock |\n| Parsimony Sites | FASTA\u002FPHYLIP | Sites with >=2 chars appearing >=2 times |\n\n---\n\n## Common Patterns\n\n### Single Metric Across Groups\n```python\nfungi_dvmc = batch_dvmc(discover_gene_files(\"data\u002Ffungi\"))\nanimal_dvmc = batch_dvmc(discover_gene_files(\"data\u002Fanimals\"))\nprint(f\"Fungi median: {np.median(list(fungi_dvmc.values())):.4f}\")\n```\n\n### Statistical Comparison\n```python\nu_stat, p_value = stats.mannwhitneyu(list(g1.values()), list(g2.values()), alternative='two-sided')\n```\n\n### Filtering + Metric\nFilter by gap percentage \u003C 5%, then compute treeness\u002FRCV on filtered set.\n\n### Batch Processing\n```python\ngene_files = discover_gene_files(\"data\u002F\")  # → [{gene_id, aln_file, tree_file}]\ntreeness_results = batch_treeness(gene_files)  # → {gene_id: value}\n```\n\n---\n\n## Answer Extraction\n\n| Pattern | Method |\n|---------|--------|\n| \"median X\" | `np.median(values)` |\n| \"maximum X\" | `np.max(values)` |\n| \"difference in median\" | `abs(np.median(a) - np.median(b))` |\n| \"Mann-Whitney U\" | `stats.mannwhitneyu(a, b)[0]` |\n| \"fold-change\" | `np.median(a) \u002F np.median(b)` |\n\n**Rounding**: PhyKIT default 4 decimals. U stats = integer. Question wording overrides.\n\n---\n\n## Interpretation\n\n| Metric | Good | Acceptable | Poor |\n|--------|------|-----------|------|\n| Treeness | >0.8 | 0.5-0.8 | \u003C0.5 |\n| RCV | \u003C0.2 | 0.2-0.5 | >0.5 |\n| Treeness\u002FRCV | >2.0 | 1.0-2.0 | \u003C1.0 |\n| Bootstrap | >95% | 70-95% | \u003C70% |\n| Parsimony sites | >30% | 10-30% | \u003C10% |\n\n## Completeness Checklist\n\nAll files identified; group structure detected; correct PhyKIT function; ALL genes processed (not sample); correct test; 4-decimal rounding; specific statistic (median\u002Fmax\u002FU\u002Fp); Mann-Whitney `alternative='two-sided'`.\n\n---\n\n## References\n\n`references\u002Fsequence_alignment.md`, `references\u002Ftree_building.md`, `references\u002Fparsimony_analysis.md`, `scripts\u002Ftree_statistics.py`\n- PhyKIT: https:\u002F\u002Fjlsteenwyk.com\u002FPhyKIT\u002F\n- Biopython Phylo: https:\u002F\u002Fbiopython.org\u002Fwiki\u002FPhylo\n- DendroPy: 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