Introduction

• Why IQ-TREE?
• Key features
• Free web server
• User support
• Documentation
• How to cite IQ-TREE?
• Development team
• Credits and acknowledgements

→ Read All Introduction Here

Getting Started

Recommended for users who just downloaded IQ-TREE the first time.

• IQ-TREE web server
• Installation
• For Windows users
• For Mac OS X users
• Minimal command-line examples

→ Read All Getting Started Here

Web Server Tutorial

A quick starting guide for the IQ-TREE Web Server.

• Tree Inference
• Model Selection
• Analysis Results

→ Read All Web Server Tutorial Here

Beginner's Tutorial

This tutorial gives a beginner's guide.

• Input data
• First example
• Model selection
• Using codon models
• Binary, Morphological, SNPs
• Ultrafast bootstrap
• Reducing impact of severe model violations with UFBoot
• Nonparametric bootstrap
• Single branch tests
• Utilizing multi-core CPUs

→ Read All Beginner's Tutorial Here

Advanced Tutorial

Recommended for experienced users to explore more features.

• Partitioned analysis
• Partitioning with mixed data
• Partition scheme selection
• Bootstrapping partition model
• Constrained tree search
• Tree topology tests
• Testing constrained tree
• Consensus construction and bootstrap value assignment
• User-defined models
• Inferring site-specific rates

→ Read All Advanced Tutorial Here

Assessing Phylogenetic Assumptions

This guide is about evaluating the suitability of the data for phylogenetic analysis.

• Tests of symmetry
• Likelihood mapping

→ Read All Assessing Phylogenetic Assumptions Here

Concordance Factor

Gene and site concordance factor computation.

• Inferring species tree
• Inferring gene/locus trees
• Gene concordance factor (gCF)
• Site concordance factor (sCF)
• Putting it all together

→ Read All Concordance Factor Here

Phylogenetic Dating

Inferring time trees

• Bayesian dating with MCMCtree
• IQ2MC workflow for time tree inference
• Estimating the gradients and the Hessian for MCMCtree dating
• Using partitions and Mixture models for approximate likelihood dating
• How to run MCMCtree
• Least Square Dating (LSD2)
• Inferring time tree with tip dates
• Calibrating tree using ancestral dates
• Dating an existing tree
• Obtaining confidence intervals
• Excluding outlier taxa/nodes
• Full list of LSD2 options

→ Read All Phylogenetic Dating Here

LSD2 commands

All LSD2 command

→ Read All LSD2 commands Here

Rooting phylogenies

Inferring rooted trees using non-reversible models.

• Inferring unrooted tree with outgroup
• Inferring rooted trees without outgroup
• Testing root positions

→ Read All Rooting phylogenies Here

Simulating sequence alignments

Simulating sequence alignments

• Simulating an alignment from a tree and model
• Simulating other datatypes
• Non-reversible models
• Rate heterogeneity across sites
• Customizing output alignments
• Insertion and deletion models
• Specifying model parameters
• Mimicking a real alignment
• Simulating along a random tree
• Branch-specific models
• Partition models
• Mixture models
• Heterotachy GHOST model
• Functional divergence model
• Pre-define mutations
• Parallel sequence simulations
• Command reference

→ Read All Simulating sequence alignments Here

Frequently Asked Questions

For common questions and answers.

• How do I get help?
• How do I report bug?
• How to interpret ultrafast bootstrap (UFBoot) supports?
• How does IQ-TREE treat gap/missing/ambiguous characters?
• Can I mix DNA and protein data in a partitioned analysis?
• What is the interpretation of branch lengths when mixing codon and DNA data?
• What is the purpose of composition test?
• What is the good number of CPU cores to use
• How do I save time for standard bootstrap?
• Why does IQ-TREE complain about the use of +ASC model?
• How does IQ-TREE treat identical sequences?

→ Read All Frequently Asked Questions Here

Recipes (How-To)

Collection of examples that combine IQ-TREE with other software.

• Phylogenetic placement
• Perform a Goldman-Cox test
• Estimating gene, site, and quartet concordance vectors
• Simulating concatenated alignments with multiple trees

→ Read All Recipes (How-To) Here

Substitution Models

All common substitution models and usages.

• DNA models
• Protein models
• Codon models
• Binary, morphological models
• Ascertainment bias correction
• Rate heterogeneity across sites

→ Read All Substitution Models Here

Complex Models

Complex models such as partition and mixture models.

• Partition models
• Mixture models
• Site-specific frequency models
• Heterotachy models
• Multitree models

→ Read All Complex Models Here

Estimating amino acid substitution models

Estimating amino acid substitution models.

• Estimating a model from a single concatenated alignment
• Estimating a model from a folder of alignments
• Estimating a non-reversible model
• Estimating linked exchangeabilities

→ Read All Estimating amino acid substitution models Here

Polymorphism-Aware Models

Improve inferences using population data.

• Counts files
• First example
• Substitution models
• Virtual population size
• Sampling method
• Bootstrap branch support
• Interpretation of branch lengths

→ Read All Polymorphism-Aware Models Here

Command Reference

Commprehensive documentation of command-line options.

• General options
• Checkpointing to resume stopped run
• Likelihood mapping analysis
• Automatic model selection
• Specifying substitution models
• Rate heterogeneity
• Partition model options
• Site-specific frequency model options
• Tree search parameters
• Tree search for pathogen data
• Ultrafast bootstrap parameters
• Nonparametric bootstrap
• Single branch tests
• Ancestral sequence reconstruction
• Tree topology tests
• Constructing consensus tree
• Robinson-Foulds distance
• Generating random trees
• Miscellaneous options

→ Read All Command Reference Here

Compilation Guide

For advanced users to compile IQ-TREE source code.

• General requirements
• Downloading source code
• Compiling under Linux
• Compiling under Mac OS X
• Compiling under Windows
• Compiling 32-bit version
• Compiling MPI version
• Compiling Xeon Phi Knights Landing version
• About precompiled binaries

→ Read All Compilation Guide Here

Developer Guide

This guide gives developers an overview of IQ-TREE software design, data structures and discusses possibility to incorporate new models into IQ-TREE.

• Alignment
• Model of substitution
• PhyloTree class

→ Read All Developer Guide Here

Analyzing Big Data

Hints and strategies to analyze big alignments with >= 1000 sequences or >= 10,000 sites.

→ Read All Analyzing Big Data Here