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Phylogenetics Pipeline

Runs the standard phylogenetics workflow — MAFFT alignment, IQ-TREE 2/FastTree inference, and ETE3 tree analysis and rendering.

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

What it does

  • Multiple sequence alignment: MAFFT wrapper with method presets (linsi, einsi, fftnsi, fftns, auto) chosen by dataset size
  • Alignment trimming: TrimAl (automated1/gappyout/strict) with automatic fallback to the untrimmed alignment
  • Tree inference: IQ-TREE 2 with automatic model selection (-m TEST) and ultrafast bootstrap (-B 1000), or FastTree for very large datasets
  • Tree analysis & visualization: ETE3 helpers for Newick loading, leaf/branch-length statistics, MRCA lookup, pruning, midpoint rooting, and PNG rendering with support values
  • Reference tables: DNA and protein substitution model guides (GTR+G4, HKY+G4, LG+G4, WAG, JTT, Q.pfam) plus practical best practices

Who it's for

  • Microbial genomics researchers building 16S rRNA or core-genome species trees
  • Viral phylodynamics and molecular-clock analysts (e.g., SARS-CoV-2 lineages)
  • Evolutionary bioinformaticians studying protein families, HGT, or ancestral sequence reconstruction

Examples

  1. "Align this gene FASTA and build an ML tree with 1000 bootstraps" → MAFFT auto → IQ-TREE model TEST → annotated PNG with support values
  2. "I have 8,000 sequences and IQ-TREE is too slow" → switch to use_fasttree=True for FastTree GTR mode
  3. "No outgroup known — root the tree and color specific clades" → midpoint rooting plus color_groups rendering

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/phylogenetics/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

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 AI 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 && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/phylogenetics ~/.claude/skills/

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

  1. Create the skills folder: mkdir -p ~/.claude/skills
  2. Clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  3. Copy the skill: cp -r scientific-agent-skills/skills/phylogenetics ~/.claude/skills/
  4. Install the CLI tools (conda recommended): conda install -c bioconda mafft iqtree fasttree trimal
  5. Install Python deps: pip install ete3 PyQt5 (PyQt5 is required for image rendering)
  6. Verify with mafft --version, iqtree2 --version, and FastTree
  7. Restart Claude Code and ask something like "build a phylogenetic tree from this FASTA file" to trigger the skill.
View source on GitHub ↗License: MIT