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Phylogenetic Tree Builder

Builds and reads evolutionary trees from DNA or protein sequences using MAFFT, IQ-TREE and FastTree.

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
3 files

What it does

Once installed, the agent follows a structured workflow for estimating evolutionary relationships between related DNA or protein sequences. It lines the sequences up with MAFFT, infers a tree with IQ-TREE (or FastTree as a faster approximation), and reports branch support values so you can judge how reliable each branch is. It also warns about common mistakes, such as treating a gene tree as a species tree or dating trees from sampling dates alone.

Great for

  • Researchers comparing a gene or protein family across several organisms
  • Microbiology labs building gene trees from their own sequence data
  • Students learning how alignment, model selection and branch support fit together

Skip it if

  • Clinical or public-health conclusions drawn from a single tree, since the skill itself cautions that trees do not establish transmission or species history alone
  • Users who lack the external MAFFT and IQ-TREE (or FastTree) programs installed, because the skill only orchestrates them and cannot run without them

Try asking

  • “Build a maximum likelihood tree from my aligned protein sequences in proteins.fasta using ModelFinder and 1000 bootstrap replicates”
  • “Align these nucleotide sequences with MAFFT and infer a tree, then summarise the branch support”
  • “Re-run the tree inference on my reviewed alignment without realigning it”
Step-by-step guide: how to use Phylogenetic Tree BuilderInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 3 original files, the MIT licence and an attribution note.

    phylogenetics.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip phylogenetics.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip phylogenetics.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Use --type nt or --type aa explicitly and check that FASTA IDs are unique and free of spaces before running.
  • Read the .iqtree and .log report files rather than relying on the picture alone, and remember that UFBoot and SH-aLRT thresholds are screening guides, not proof.
  • Use a new output prefix when your data or model assumptions change, because IQ-TREE keeps checkpoints and only --redo overwrites results.

What's inside

  • references/iqtree_inference.md
  • scripts/phylogenetic_analysis.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.