How do I install the Iqtree3 skill?

Run npx skillmds@latest add vimalinx/iqtree3 in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Iqtree3 safe to use?

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Which AI agents work with Iqtree3?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Iqtree3 free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Iqtree3?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Iqtree3 by vimalinx — Agent Skill

Name: Iqtree3
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

iqtree3

Quick Start

Command: iqtree3 -s ALIGNMENT [-m MODEL] [-B 1000]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/iqtree3
Full reference: references/help.md

When To Use This Tool

Infer maximum-likelihood phylogenetic trees from aligned DNA, protein, codon, morphology, or partitioned data.
Select substitution models with ModelFinder before or during tree search.
Add branch support with ultrafast bootstrap, non-parametric bootstrap, SH-aLRT, or related support tests.
Run partitioned analyses, topology tests, likelihood mapping, or concordance-factor workflows in one phylogenetic engine.

Common Patterns

# 1) Model selection plus ML tree with ultrafast bootstrap support
iqtree3 \
  -s alignment.fasta \
  -m MFP \
  -B 1000 \
  --alrt 1000 \
  -T AUTO

# 2) Partitioned phylogeny with a partition file
iqtree3 \
  -s concatenated.phy \
  -p partitions.nex \
  -m MFP \
  -B 1000 \
  -T AUTO

# 3) Likelihood mapping to inspect phylogenetic signal
iqtree3 \
  -s alignment.fasta \
  --lmap 10000

Recommended Workflow

Prepare input alignment in a supported format (PHYLIP, FASTA, NEXUS, CLUSTAL, or MSF)
Run ModelFinder to identify best-fit model: iqtree3 -s alignment.fasta -m MF
Infer tree with branch support: iqtree3 -s alignment.fasta -m MODEL -B 1000 --alrt 1000
Examine output files (.treefile, .iqtree, .log) and checkpoint options (--redo, --undo) if re-running

Guardrails

Always specify an alignment via -s; IQ-TREE requires input data to run
Use -T AUTO or explicit thread count to avoid oversubscribing CPUs
-B ultrafast bootstrap is intended for large replicate counts; 1000 is the usual minimum practical setting
Check the .iqtree report and .log for convergence, composition, or numerical warnings before trusting the tree

---name: iqtree3description: Use when inferring maximum-likelihood phylogenetic trees, selecting substitution models, running bootstrap support analyses, or performing partitioned phylogenetic analyses on sequence alignments.---# iqtree3## Quick Start- Command: `iqtree3 -s ALIGNMENT [-m MODEL] [-B 1000]`- Local executable: `/home/vimalinx/miniforge3/envs/bio/bin/iqtree3`- Full reference: `references/help.md`## When To Use This Tool- Infer maximum-likelihood phylogenetic trees from aligned DNA, protein, codon, morphology, or partitioned data.- Select substitution models with ModelFinder before or during tree search.- Add branch support with ultrafast bootstrap, non-parametric bootstrap, SH-aLRT, or related support tests.- Run partitioned analyses, topology tests, likelihood mapping, or concordance-factor workflows in one phylogenetic engine.## Common Patterns```bash# 1) Model selection plus ML tree with ultrafast bootstrap supportiqtree3 \ -s alignment.fasta \ -m MFP \ -B 1000 \ --alrt 1000 \ -T AUTO``````bash# 2) Partitioned phylogeny with a partition fileiqtree3 \ -s concatenated.phy \ -p partitions.nex \ -m MFP \ -B 1000 \ -T AUTO``````bash# 3) Likelihood mapping to inspect phylogenetic signaliqtree3 \ -s alignment.fasta \ --lmap 10000```## Recommended Workflow1. Prepare input alignment in a supported format (PHYLIP, FASTA, NEXUS, CLUSTAL, or MSF)2. Run ModelFinder to identify best-fit model: `iqtree3 -s alignment.fasta -m MF`3. Infer tree with branch support: `iqtree3 -s alignment.fasta -m MODEL -B 1000 --alrt 1000`4. Examine output files (`.treefile`, `.iqtree`, `.log`) and checkpoint options (`--redo`, `--undo`) if re-running## Guardrails- Always specify an alignment via `-s`; IQ-TREE requires input data to run- Use `-T AUTO` or explicit thread count to avoid oversubscribing CPUs- `-B` ultrafast bootstrap is intended for large replicate counts; `1000` is the usual minimum practical setting- Check the `.iqtree` report and `.log` for convergence, composition, or numerical warnings before trusting the tree

Frequently asked questions

Iqtree3