Skip to main content
affpapa.org
RU EN
skill Claude Code CX Codex Cursor GitHub Copilot

phylogenetics — Claude Code skill: build phylogenetic trees

Skill for aligning DNA and protein sequences, inferring phylogenetic trees with branch support calculation, and visualizing results. For researchers in bioinformatics, microbiology, and molecular evolution.

Install into Claude Code · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add K-Dense-AI/scientific-agent-skills --skill phylogenetics -a claude-code
Open on GitHub

What phylogenetics does

The skill uses MAFFT for aligning homologous sequences, IQ-TREE for maximum likelihood tree inference with automated model selection (ModelFinder) and branch support (UFBoot and SH-aLRT), and FastTree as a faster alternative. Results are visualized and summarized through ETE3.

Inside the skill is a Python script, phylogenetic_analysis.py, wrapping these bioinformatics tools. You specify sequence type (DNA or protein), thread count, and bootstrap replicates; the rest is automated. IQ-TREE by default searches the full model space (-m MFP) with 1000 UFBoot replicates and SH-aLRT test; FastTree runs faster but with less thorough search.

Requires installed MAFFT, IQ-TREE 3 (or IQ-TREE 2 with a flag), and FastTree. Optional: Python 3.12, ete3 3.1.3, and PyQt5 for visualization; trimAl for alignment trimming. All computation is local; network access needed only for package installation. Important: ETE3 imports cgi, removed in Python 3.13, so Python 3.12 is required.

What it helps with

  • align homologous sequences into a multiple alignment
  • infer a phylogenetic tree with branch support metrics
  • select the best-fit substitution model and test alternatives
  • visualize the tree and interpret support values

Example prompts for the agent

  • Align sequences from sequences.fasta using MAFFT and build a maximum likelihood tree
  • Using the alignment aligned.fasta, infer a phylogenetic tree for DNA sequences with 1000 bootstrap replicates
  • Build a tree for protein sequences with the fast approximate method FastTree and calculate branch support

How to install phylogenetics

1Skills CLI (Vercel)

npx skills add K-Dense-AI/scientific-agent-skills --skill phylogenetics -a claude-code

2Manually: put the files in place

~/.claude/skills/phylogenetics/SKILL.md

Copy the whole skill folder; for one project use .claude/skills/phylogenetics/

From the same set120

The whole set →
scientific-visualization K-Dense-AI Generates and audits publication-ready scientific figures in Matplotlib, Seaborn, and Plotly, focusing on truthful data encoding and accessibility. Claude Code CX Codex Cursor +1 2,400installs scientific-writing K-Dense-AI This skill drafts and audits scientific manuscripts and reports while tying claims to verified evidence. Use it for sections, references, declarations, and submission checks. Claude Code CX Codex Cursor +1 2,400installs statistical-analysis K-Dense-AI Runs hypothesis tests with assumption checking, effect sizes, and APA-formatted reports. Covers t-tests, ANOVA, correlation, regression, non-parametric and Bayesian methods. Claude Code CX Codex Cursor +1 2,300installs scientific-brainstorming K-Dense-AI Structures early-stage research ideation through independent idea generation, transparent scoring, and adversarial review. Useful for ranking hypotheses without premature consensus. Claude Code CX Codex Cursor +1 2,300installs literature-review K-Dense-AI This skill searches and synthesizes research literature, checks citations, and prepares Markdown or PDF reviews. Use it for reproducible searches and screening. Claude Code CX Codex Cursor +1 2,300installs scientific-critical-thinking K-Dense-AI Evaluates scientific claims, research methodology, and evidence quality. Applies GRADE and Cochrane Risk of Bias frameworks. Claude Code CX Codex Cursor +1 2,300installs scientific-schematics K-Dense-AI Creates PNG drafts of scientific diagrams and runs a separate quality review. Use it for neural network architectures, flowcharts, system diagrams, and biological pathways. Claude Code CX Codex Cursor +1 2,200installs scikit-learn K-Dense-AI A skill for Python machine learning tasks: classification, regression, clustering, preprocessing, and building ML pipelines with scikit-learn 1.9.1. Claude Code CX Codex Cursor +1 2,200installs

Similar

sr-screener Imbad0202 Applies protocol-driven screening to study records for reviews. It manages double-blind screening of titles, abstracts, and full texts. Claude Code CX Codex Cursor +1 449installs typst-author jihe520 Generates, edits, and troubleshoots Typst markup while enforcing syntax rules and formatting checks. Keeps agents grounded against hallucinations. Claude Code CX Codex Cursor +1 1,800installs anysearch anysearch-ai This skill gives an agent web search, domain-specific queries, parallel batch search, and page extraction. Use it when a task needs current information or a claim needs checking. Claude Code CX Codex Cursor +1 38,500installs academic-paper Imbad0202 This skill runs a 12-agent academic pipeline across 11 modes. It guides projects from literature searches and outlines to citation audits and rebuttal reviews. Claude Code CX Codex Cursor +1 10,800installs nature-figure Yuan1z0825 A skill that builds, revises and audits scientific figures for manuscripts in Python or R. Useful when plots go to submission, not to a report. Claude Code CX Codex Cursor +1 18,700installs academic-paper-reviewer Imbad0202 This skill reviews an academic paper through five role-based perspectives. Use it for peer review, revision checks, or a focused methodology assessment. Claude Code CX Codex Cursor +1 9,800installs nature-polishing Yuan1z0825 A skill that polishes, translates and tightens existing academic prose. Facts, terminology and evidence boundaries stay intact. Claude Code CX Codex Cursor +1 17,400installs nature-citation Yuan1z skill, refactored into static/dynamic layers Finds Nature and CNS-family papers for manuscript claims, maps claims to sources, and prepares a reference-manager export. Use it when the journal scope matters. Claude Code CX Codex Cursor +1 15,600installs

Questions about phylogenetics

How do I install phylogenetics in Claude Code?

Run npx skills add K-Dense-AI/scientific-agent-skills --skill phylogenetics -a claude-code, then locate the skill documentation at ~/.claude/skills/phylogenetics/SKILL.md.

What does phylogenetics do?

The skill automates a bioinformatics workflow: aligns sequences (MAFFT), builds a maximum likelihood tree (IQ-TREE) with model selection and branch support calculation, or uses fast approximate inference (FastTree), and visualizes the results.

What Python version does phylogenetics require?

Python 3.12 for full visualization features (ETE3 3.1.3). Core tree inference runs with installed MAFFT and IQ-TREE independently. Python 3.13 removed the cgi module that ETE3 needs.

See also

Project sponsors

Companies that keep this analytics open
Gold sponsor
Nutra.Club

Impressions, clicks and code copies — open statistics. We keep the numbers public for the same reason NeBlask itself is public. Become a sponsor