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