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IQ-TREE: Phylogenomic inference software


Dear All,

I’m not sure whether it is still proper to post this here: We created and are actively developing the IQ-TREE open-source software for phylogenomic inference at IQ-TREE is especially suited to analyze NGS data and has perhaps the most comprehensive sets of maximum likelihood models available to date incl. common DNA, protein, codon models as well as complex partition, mixture, CAT, heterotachy models, etc. IQ-TREE offers fast tree search, model selection (ModelFinder), ultrafast bootstrapping (UFBoot) and many other features.

IQ-TREE has a good documentation (, user support ( and a free online web service (

IQ-TREE is the successor of the IQPNNI and TREE-PUZZLE software.

Kind regards, Minh and the development team.


We (The HIV Databases team at LANL) have put up an IQ-TREE server here. It has one feature that is not available at the link Bui Quang Minh provided above; it will out put the site-specific rates file if you use a heterogeneous rates model and click the check box to output the file.


We added another feature this week. Now you can download the alignment in “tree order” as one of the results options.


Dear community,

We are pleased to announce the major release 1.6.0 of the IQ-TREE software ( Among others, notable new features include:

  • Many new realistic models of sequence evolution: Heterotachy, Lie Markov and Polymorphism-aware Models.
  • Improved ModelFinder allowing to test above models. For partitioned analysis ModelFinder now supports edge-linked partition model selection and fast relaxed clustering algorithm (-rclusterf option) like PartitionFinder2.
  • A fast tree search option to match the speed of FastTree while still obtaining better trees (-fast option).
  • Ancestral sequence reconstruction (-asr option).
  • An option to reduce the impact of model violation for the ultrafast bootstrap (-bnni option).
  • Xeon Phi Knights Landing (AVX-512 instruction set) support.

Kind regards,

IQ-TREE development team