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

1. 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