Phylogenetics

What it does

When your agent uses it

• Tasks that involve Bioinformatics

Example prompts

• “Use the phylogenetics skill to build and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with…”
• “/phylogenetics”

Requirements

• Python 3
• Compatibility (from SKILL.md): Requires MAFFT and IQ-TREE 3 or FastTree executables. Optional tree summaries use Python 3.12 and ete3 3.1.3; rendering also needs PyQt5. Optional trimming needs trimAl. Network access is required for installation, not local inference.

Workflow steps

5 steps, taken from the step headings in SKILL.md.

1. 1Establish the biological input
2. 2Align and inspect
3. 3Infer a tree
4. 4Interpret support, rooting and outputs
5. 5Summarize and visualize

What it can do on your machine

Read from SKILL.md and the folder at commit 92ace75. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships 1 file in scripts/ (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • uv
  • python
  • conda

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • mafft.cbrc.jp
  • iqtree.github.io
  • etetoolkit.org
  • github.com
  • morgannprice.github.io
  • vicfero.github.io

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

• Compatibility

  Requires MAFFT and IQ-TREE 3 or FastTree executables. Optional tree summaries use Python 3.12 and ete3 3.1.3; rendering also needs PyQt5. Optional trimming needs trimAl. Network access is required for installation, not local inference.

  From compatibility in the SKILL.md frontmatter.

Context cost

Phylogenetics loads about 2.3k tokens when it runs, and up to ~4.2k if it reads all its reference files. Until then it costs about 96 tokens; SKILL.md has 853 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~96

When it runs · the whole SKILL.md, loaded when a task matches

~2.3k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~4.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from K-Dense-AI/scientific-agent-skills at commit 92ace75, republished under its MIT licence (© K-Dense-AI). 853 words, ~2,347 tokens.

name

phylogenetics

description

Builds and analyzes phylogenetic trees using MAFFT multiple sequence alignment, IQ-TREE maximum likelihood with ModelFinder and branch support, and FastTree approximate inference. Uses ETE3 for tree summaries and visualization. Applies to homologous nucleotide or protein sequences, microbial gene trees, protein families, and cautiously interpreted dated phylogenies.

compatibility

Requires MAFFT and IQ-TREE 3 or FastTree executables. Optional tree summaries use Python 3.12 and ete3 3.1.3; rendering also needs PyQt5. Optional trimming needs trimAl. Network access is required for installation, not local inference.

license

Unknown

metadata.version

1.5

metadata.skill-author

Kuan-lin Huang

metadata.last-reviewed

2026-10-01

conda create -n phylo -c conda-forge -c bioconda mafft iqtree fasttree trimal
conda activate phylo
uv venv --python 3.12 .venv-phylo
uv pip install --python .venv-phylo/bin/python ete3==3.1.3 numpy six
# Optional rendering backend; it can require a working Qt platform plugin.
uv pip install --python .venv-phylo/bin/python PyQt5

mafft --auto --thread 1 --inputorder sequences.fasta > aligned.fasta
# L-INS-i: locally alignable homologs, typically small datasets.
mafft --localpair --maxiterate 1000 --thread 1 --inputorder sequences.fasta > linsi.fasta
# E-INS-i: homologs with large internal gaps.
mafft --genafpair --maxiterate 1000 --thread 1 --inputorder sequences.fasta > einsi.fasta
# FFT-NS-i (two refinement cycles), then FFT-NS-2 (progressive).
mafft --retree 2 --maxiterate 2 --thread 1 --inputorder sequences.fasta > fftnsi.fasta
mafft --retree 2 --maxiterate 0 --thread 1 --inputorder sequences.fasta > fftns.fasta

trimal -in aligned.fasta -out trimmed.fasta -automated1 -fasta

python scripts/phylogenetic_analysis.py sequences.fasta --type nt --threads 1 \
  --bootstrap 1000 --seed 42 --output-dir results --no-visualization
# Use a reviewed alignment (including any explicit trimming) without realigning.
python scripts/phylogenetic_analysis.py aligned.fasta --aligned --type nt \
  --threads 1 --output-dir reviewed --no-visualization
# Protein FastTree alternative; --threads applies to MAFFT/IQ-TREE, not FastTree.
python scripts/phylogenetic_analysis.py proteins.fasta --type aa --fasttree \
  --threads 1 --output-dir fast_protein --no-visualization

# Run from the skill directory in the ETE3 environment.
import sys
sys.path.insert(0, "scripts")
from phylogenetic_analysis import load_tree, tree_summary

tree = load_tree("results/sequences.treefile")
print(tree.get_leaf_names())
print(tree_summary("results/sequences.treefile"))

© K-Dense-AI, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 2 other files (scripts, references) in skills/phylogenetics of K-Dense-AI/scientific-agent-skills.

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

Open the folder on GitHubat commit 92ace75

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in K-Dense-AI/scientific-agent-skills, which our catalogue first saw on October 7, 2026.

• lingxling/awesome-skills-cnclaude-scientific-skills/skills/phylogenetics