Last update: Dec 1, 2019, Contributors: Jana Trifinopoulos, M Bui, Minh Bui, Nltung
Thanks to the recent advent of next-generation sequencing techniques, the amount of phylogenomic/transcriptomic data have been rapidly accumulated. This extremely facilitates resolving many “deep phylogenetic” questions in the tree of life. At the same time it poses major computational challenges to analyze such big data, where most phylogenetic software cannot handle. Moreover, there is a need to develop more complex probabilistic models to adequately capture realistic aspects of genomic sequence evolution.
This trends motivated us to develop the IQ-TREE software with a strong emphasis on phylogenomic inference. Our goals are:
IQ-TREE has been developed since 2011 and freely available at http://www.iqtree.org/ as open-source software under the GNU-GPL license version 2. It is actively maintained by the core development team (see below) and a number of collabrators.
The strength of IQ-TREE is the availability of a wide variety of phylogenetic models:
For a quick start you can also try the IQ-TREE web server, which performs online computation using a dedicated computing cluster. It is very easy to use with as few as just 3 clicks! Try it out at
Please refer to the user documentation and frequently asked questions. If you have further questions, feedback, feature requests, and bug reports, please sign up the following Google group (if not done yet) and post a topic to the
The average response time is two working days.
IQ-TREE has an extensive documentation with several tutorials and manual:
To maintain IQ-TREE, support users and secure fundings, it is important for us that you cite the following papers, whenever the corresponding features were applied for your analysis.
Example 1: We obtained branch supports with the ultrafast bootstrap (Hoang et al., 2018) implemented in the IQ-TREE software (Nguyen et al., 2015).
Example 2: We inferred the maximum-likelihood tree using the edge-linked partition model in IQ-TREE (Chernomor et al., 2016; Nguyen et al., 2015).
If you performed the tests of symmetry, please cite:
If you used the polymorphism-aware models please cite:
If you used the heterotachy model (GHOST) please cite:
If you performed the ultrafast bootstrap (UFBoot) please cite:
If you used posterior mean site frequency model please cite:
If you used ModelFinder please cite:
If you performed tree reconstruction please cite:
If you used partition models e.g., for phylogenomic analysis please cite:
If you used the IQ-TREE web server please cite:
IQ-TREE is actively developed by:
Bui Quang Minh, Team leader, Designs and implements software core, tree search, ultrafast bootstrap, model selection.
Robert Lanfear, Co-leader, Model selection.
Olga Chernomor, Developer, Implements partition models.
Heiko A. Schmidt, Developer, Integrates TREE-PUZZLE features.
Dominik Schrempf, Developer, Implements polymorphism-aware models (PoMo).
Michael Woodhams, Developer, Implements Lie Markov models.
Diep Thi Hoang, Developer, Improves ultrafast bootstrap.
Arndt von Haeseler, Advisor.
Lam Tung Nguyen, Developer, Implemented tree search algorithm.
Jana Trifinopoulos, Developer, Implemented web service.
Some parts of the code were taken from the following packages/libraries: Phylogenetic likelihood library, TREE-PUZZLE, BIONJ, Nexus Class Libary, Eigen library, SPRNG library, Zlib library, gzstream library, vectorclass library, GNU scientific library.
IQ-TREE was funded by the Austrian Science Fund (grant no. I760-B17 from 2012-2015 and I 2508-B29 from 2016-2017), the University of Vienna (Initiativkolleg I059-N from 2012-2015), the Australian National University (2018-onwards), Chan-Zuckerberg Initiative (2020).