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.
Gene and site concordance factor computation.
Commprehensive documentation of command-line options.
For common questions and answers.
All common substitution models and usages.
Complex models such as partition and mixture models.
Improve inferences using population data.
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.