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