Claude Skill MartBrowse skillsWhat is a Skill?
 
← Back to list

Phylogenetics

An end-to-end phylogenetics pipeline: MAFFT alignment, IQ-TREE 2 / FastTree ML inference, and ETE3 tree analysis and plotting.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 8/10Last updated: Aug 9, 2026

What it does

Packages the standard molecular phylogenetics workflow into ready-to-run Python helpers so Claude can go from raw sequences to a publication-ready tree.

  • MAFFT multiple sequence alignment with a mode-selection guide (linsi/einsi for small sets, fftnsi, fftns, auto for large ones)
  • TrimAl trimming of unreliable alignment columns, with graceful fallback to the untrimmed alignment
  • IQ-TREE 2 maximum likelihood trees with automatic model selection (-m TEST), 1000 ultrafast bootstraps, and molecular-clock (--date) hints
  • FastTree for datasets of thousands of sequences where full ML is too slow
  • ETE3 analysis/visualization: tree stats, MRCA lookup, midpoint rooting, pruning, per-taxon coloring, PNG rendering
  • Model cheat-sheets for DNA (GTR, HKY, TrN, JC) and protein (LG, WAG, JTT, Q.pfam) plus best-practice checklist (alignment quality, rooting, recombination screening)

Who it's for

  • Microbial genomics researchers building 16S or core-genome species trees
  • Viral phylodynamics analysts tracing outbreak spread and divergence dates
  • Grad students working on protein family evolution, HGT detection, or ancestral sequence reconstruction
  • Bioinformatics engineers tired of rewriting the same align→trim→tree glue code

Examples

  1. One-shot pipeline: ask "build a tree from spike.fasta" and full_phylogenetic_analysis() produces the alignment, treefile, midpoint-rooted Newick, and a PNG inside phylo_results/.
  2. Scale switch: with 8,000 sequences, set use_fasttree=True to get an approximate ML tree 10–100× faster than IQ-TREE.
  3. Figure polishing: pass color_groups to paint clinical isolates red and reference strains blue while showing bootstrap support on a rectangular layout.

· · · Install guide · · ·

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/phylogenetics folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/phylogenetics/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills && mkdir -p ~/.claude/skills && cp -r /tmp/scientific-agent-skills/skills/phylogenetics ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Copy the skill folder into Claude's skills directory: mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/phylogenetics ~/.claude/skills/
  3. Install the command-line tools (conda recommended): conda install -c bioconda mafft iqtree fasttree trimal
  4. Install the Python libraries: uv pip install ete3 matplotlib (or use pip install ...)
  5. If you need PNG tree images, also install the Qt backend: uv pip install PyQt5
  6. Verify the tools respond: mafft --version, iqtree2 --version, and FastTree.
  7. Restart Claude Code, then say something like "build a phylogenetic tree from this FASTA" and the skill will trigger automatically.
View source on GitHub ↗License: MIT