Recommended for users who just downloaded IQ-TREE the first time.
A quick starting guide for the IQ-TREE Web Server.
This tutorial gives a beginner's guide.
Recommended for experienced users to explore more features.
This guide is about evaluating the suitability of the data for phylogenetic analysis.
Gene and site concordance factor computation.
Building time tree with node dates on phylogenetic trees.
Estimating amino acid substitution models.
Inferring rooted trees using non-reversible models.
Simulating sequence alignments
For common questions and answers.
All common substitution models and usages.
Complex models such as partition and mixture models.
Improve inferences using population data.
Commprehensive documentation of command-line options.
For advanced users to compile IQ-TREE source code.
This guide gives developers an overview of IQ-TREE software design, data structures and discusses possibility to incorporate new models into IQ-TREE.
Hints and strategies to analyze big alignments with >= 1000 sequences or >= 10,000 sites.