iqtree

name	iqtree
description	Use when inferring maximum-likelihood phylogenies from aligned sequences, performing automated model selection, or assessing branch support with bootstrap or aLRT methods
disable-model-invocation	true
user-invocable	true

iqtree

Quick Start

• Command: iqtree -s ALIGNMENT -m MODEL
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/iqtree
• Version: 3.0.1
• Full options: see references/help.md

When To Use This Tool

• Infer a maximum-likelihood phylogeny from an existing alignment.
• Run ModelFinder to choose a substitution model.
• Estimate branch support with ultrafast bootstrap or SH-aLRT.
• Use partition-aware analyses when the dataset contains multiple loci or predefined partitions.

Common Patterns

# 1) ModelFinder plus tree inference
iqtree -s alignment.fasta -m MFP

# 2) Tree inference with support values
iqtree -s alignment.fasta -m GTR+F+R4 -B 1000 --alrt 1000 -T AUTO

# 3) Partitioned analysis
iqtree -s alignment.fasta -p partitions.nex -m MFP -T AUTO

Recommended Workflow

1. Start from a trustworthy multiple-sequence alignment.
2. Run model selection unless a justified model is already fixed by protocol.
3. Add branch support estimation in the same run or a well-documented follow-up run.
4. Inspect .iqtree, .treefile, and support values before making biological claims.

Guardrails

• IQ-TREE does not align sequences; garbage alignments produce garbage trees.
• -B ultrafast bootstrap is intended for large replicate counts, commonly >=1000.
• Use -T AUTO and --mem thoughtfully on shared machines.
• Model choice, support values, and partition strategy are part of the inference, not optional cosmetics.