domains / science / phylogenetic-tree-inference / phylogenetics

phylogenetics

Skill card

combined

The two copies describe the same MAFFT/IQ-TREE/FastTree/ETE3 pipeline but disagree on key parameters and operational rules. The K-Dense copy is a more rigorous, version-pinned procedure (IQ-TREE 3, MFP model, explicit FastTree flags, ETE3/Python 3.12 constraints, no silent trim fallback, bundled helper script). The OpenClaw copy is a broader, more permissive Python-subprocess wrapper (IQ-TREE 2, TEST model, --redo by default, silent trim fallback, FigTree option, different MAFFT method mapping). Crowning one would hide a real alternative workflow and conflicting defaults.

Repositories

Other copies

Combined skill

# Phylogenetics

## When to use
Use this workflow for an alignment of homologous loci or proteins, a gene tree, branch support, and an interpretable tree figure. Applies to microbial gene trees, protein families, viral phylodynamics, and cautiously interpreted dated phylogenies. A gene tree does not establish a species tree, transmission direction, or horizontal transfer by itself.

## Installation
```bash
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
uv pip install --python .venv-phylo/bin/python PyQt5
```
Verify executable versions after installation. The native executables are not Python packages.

## Workflow

### 1. Establish the biological input
- Select homologs with appropriate taxon coverage; investigate paralogs, contamination and recombination.
- Use unique, whitespace-free FASTA IDs and keep a separate sample metadata table.
- Specify `--type nt` or `--type aa` for nucleotide or protein data.
- Coding DNA needs codon-aware alignment if using a codon model.
- Keep the original sequences, accession versions, filters, alignment and exact commands.

### 2. Align and inspect
```bash
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
```
Trimming is optional and must be justified by alignment quality. If using trimAl:
```bash
trimal -in aligned.fasta -out trimmed.fasta -automated1 -fasta
```
A failed trim must stop the trimming step; do not silently copy the untrimmed input under a "trimmed" filename.

### 3. Infer a tree
Use IQ-TREE 3 with ModelFinder:
```bash
iqtree3 -s aligned.fasta -m MFP -B 1000 --alrt 1000 -T 1 --prefix results
```
Or use FastTree for approximate inference:
```bash
fasttree -nt -gtr -gamma aligned.fasta > fasttree.tree
# For proteins:
fasttree -lg -gamma proteins.fasta > fasttree_aa.tree
```
IQ-TREE checkpoints are preserved; `--redo` explicitly restarts and replaces results. Use a new output prefix when data or model assumptions change.

### 4. Summarize and visualize
Use ETE3 3.1.3 on Python 3.12 for tree summaries and visualization. ETE4 is a separate API and is not a drop-in replacement. ETE3 imports `cgi`, removed in Python 3.13.

## Conflicts
- **FreedomIntelligence/OpenClaw-Medical-Skills** uses IQ-TREE 2 with `-m TEST` and `--redo` by default, while **K-Dense-AI/scientific-agent-skills** uses IQ-TREE 3 with `-m MFP` and preserves checkpoints unless `--redo` is explicitly given.
- **FreedomIntelligence/OpenClaw-Medical-Skills** falls back to copying the untrimmed alignment on trimAl failure, while **K-Dense-AI/scientific-agent-skills** requires a failed trim to stop the trimming step.
- **FreedomIntelligence/OpenClaw-Medical-Skills** maps MAFFT methods `fftnsi`/`fftns` to `--fftnsi`/`--fftns` flags, while **K-Dense-AI/scientific-agent-skills** maps them to `--retree 2 --maxiterate 2` and `--retree 2 --maxiterate 0` respectively.
- **FreedomIntelligence/OpenClaw-Medical-Skills** includes FigTree as an optional visualization tool; **K-Dense-AI/scientific-agent-skills** does not mention FigTree.