Efficient software for phylogenomic inference

Latest version 1.6.10 (February 19, 2019)

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We are teaching IQ-TREE in various Workshops detailed here
Mesquite software 3.5 allows to run IQ-TREE with a package installed via Zephyr

IQ-TREE key features

IQ-TREE - Efficient Tree Reconstruction

A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time (Nguyen et al., 2015).

ModelFinder - Fast and Accurate Model Selection

ModelFinder (Kalyaanamoorthy et al., 2017) enables a free rate variation model and is 10 to 100 times faster than jModelTest and ProtTest. It also finds best-fit partitioning scheme like PartitionFinder.

UFBoot - Ultrafast Bootstrap Approximation

UFBoot provides approximately unbiased branch support values and runs 100X faster than nonparametric bootstrap and 10 to 40 times faster than RAxML rapid bootstrap (Minh et al., 2013).

Big Data Analysis

Supporting huge datasets with thousands of sequences or millions of alignment sites via checkpointing, safe numerical and low memory mode. Multicore CPUs and parallel MPI system are utilized to speedup analysis.

What's new in version 1.6?

IQ-TREE supports a wide range of evolutionary models

Common Models

All common substitution models for DNA, protein, codon, binary and morphological data with rate heterogeneity among sites.

Partition Models

Phylogenomic partition models allowing for mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths.

Mixture Models

Mixture models such as empirical protein mixture models and customizable mixture models.

IQ-TREE is user-friendly and well-documented

W-IQ-TREE Web Service

Easy to use web servers provided by:
Center for Integrative Bioinformatics Vienna, Austria
Los Alamos National Laboratory, USA New!

User Support

Please refer to Frequently Asked Questions. For further feedback and bug reports, please sign up and post a topic to IQ-TREE Google group.

The average response time is two working days.

User Documentation

User guide, tutorial and extensive documentation for how to use IQ-TREE.

How to cite?

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. Note that the paper of Nguyen et al. (2015) only described the tree search algorithm. Thus, it is not enough to only cite this paper if you, for example, use partition models, where Chernomor et al. (2016) should be cited.

When performing ultrafast bootstrap (UFBoot) please cite: New!

D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522.

When using posterior mean site frequency model (PMSF) please cite: New!

H.C. Wang, B.Q. Minh, S. Susko, A.J. Roger (2018) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol., 67:216–235.

When using heterotachy models please cite: New!

S.M. Crotty, B.Q. Minh, N.G. Bean, B.R. Holland, J. Tuke, L.S. Jermiin, A. von Haeseler (submitted) GHOST: Recovering historical signal from heterotachously-evolved sequence alignments. bioRxiv.

When using model selection (ModelFinder) please cite:

S. Kalyaanamoorthy, B.Q. Minh, T.K.F. Wong, A. von Haeseler, L.S. Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods, 14:587-589.

When using polymorphism-aware models please cite:

D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, C. Kosiol (2016) Reversible polymorphism-aware phylogenetic models and their application to tree inference. J. Theor. Biol., 407:362-370.

When using partition models please cite:

O. Chernomor, A. von Haeseler, B.Q. Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol., 65:997-1008.

When using IQ-TREE web server please cite:

J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.. Nucleic Acids Res., 44:W232-W235.

When performing tree reconstruction please cite:

L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies.. Mol. Biol. Evol., 32:268-274.