| name | iqtree3 |
| description | Use when inferring maximum-likelihood phylogenetic trees, selecting substitution models, running bootstrap support analyses, or performing partitioned phylogenetic analyses on sequence alignments. |
| disable-model-invocation | true |
| user-invocable | true |
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
iqtree3 \
-s alignment.fasta \
-m MFP \
-B 1000 \
--alrt 1000 \
-T AUTO
iqtree3 \
-s concatenated.phy \
-p partitions.nex \
-m MFP \
-B 1000 \
-T AUTO
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
