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About IQ-TREE

IQ-TREE is a very efficient maximum likelihood phylogenetic software with following key features among others:

A novel fast and effective stochastic algorithm to estimate maximum likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (see Nguyen et al., 2015)
An ultrafast bootstrap approximation to assess branch supports (see Minh et al., 2013).
Ultrafast and automatic model selection (10 to 100 times faster than jModelTest and ProtTest) and best partitioning scheme selection (like PartitionFinder).

The strength of IQ-TREE is the availability of a wide range of models:

All common substitution models for DNA, protein, codon, binary and morphological data.
Rate heterogeneity among sites including invariable site [+I] model, discrete Gamma [+G], and FreeRate model [+R].
Phylogenomic partition models allowing for mixed data types between partitions, linked or unlinked branch lengths, and different rate types (e.g. one partition under GTR+G and another under WAG+I+G).
Mixture models such as predefined protein mixture models (e.g., LG4X, CAT C10-C60), customizable mixture models (e.g., "MIX{HKY,GTR}"), and frequency/profile mixture models.
Ascertainment bias correction [+ASC] model for data where constant sites are missing (e.g., SNPs or morphological data).
New models can be defined and imported via a NEXUS file (see Manual).

Download

You can download source code and precompiled executables for Windows, Mac OS X and Linux, each with a sequential and a parallel multi-threaded version from here:

https://github.com/Cibiv/IQTree/releases

Installation

If you download IQ-TREE please following the Installation guide here:

https://github.com/Cibiv/IQTree/wiki/Installation

Documentation

Please read carefully before using IQ-TREE the first time or upgrading a new version!

User Manual and Tutorial 1.0

User support

If you have questions, feedback, feature requests, and bug reports, please sign up the following Google group (if not done yet) and post a topic to the

https://groups.google.com/d/forum/iqtree

The average response time is one working day.

IQ-TREE Web service

We have established a web server for online computation using a dedicated computing cluster. It is very easy to use with as few as just 3 clicks! Try it out at

http://iqtree.cibiv.univie.ac.at

Citations

To cite IQ-TREE please use:

Lam Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32, 268-274. DOI: 10.1093/molbev/msu300

To cite the ultrafast bootstrap (UFBoot) please use:

Bui Quang Minh, Minh Anh Thi Nguyen, and Arndt von Haeseler (2013) Ultrafast approximation for phylogenetic bootstrap. Mol. Biol. Evol., 30:1188-1195. DOI: 10.1093/molbev/mst024

IQ-TREE can use PLL for likelihood computations, if you use "-pll" option please cite:

T. Flouri, F. Izquierdo-Carrasco, D. Darriba, A.J. Aberer, L.-T. Nguyen, B.Q. Minh, A. von Haeseler, and A. Stamatakis (2015) The phylogenetic likelihood library. Syst. Biol., 64:356-362. DOI: 10.1093/sysbio/syu084

Acknowledgements

IQ-TREE was partially funded by the Austrian Science Fund - FWF (grant no. I760-B17 from 2012-2015) and the University of Vienna (Initiativkolleg I059-N).