Efficient phylogenomic software by maximum likelihood

Latest standard version 1.5.4 released on April 3, 2017

IQ-TREE key features

Efficient Search Algorithm

Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (Nguyen et al., 2015).

Ultrafast Bootstrap

An ultrafast bootstrap approximation (UFBoot) to assess branch supports. UFBoot is 10 to 40 times faster than RAxML rapid bootstrap and obtains less biased support values (Minh et al., 2013).

Ultrafast Model Selection

An ultrafast and automatic model selection (ModelFinder) which is 10 to 100 times faster than jModelTest and ProtTest. ModelFinder also finds best-fit partitioning scheme like PartitionFinder.

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.

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

Online Web Service

IQ-TREE web server for online computations. It is very easy to use with as few as just 3 clicks!

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.

IQ-TREE variants New!

Polymorphism-aware Models (PoMo)

PoMo models accounting for incomplete lineage sorting to infer species tree from genome-wide population data (Schrempf et al., 2016).

Download IQ-TREE PoMo User Guide

Heterotachy Models

Mixture models accounting for heterotachous evolution - rate heterogeneity among sites and lineages (Crotty et al., in prep.).

Download IQ-TREE Heterotachy User Guide

The variants are maintained separately and will be merged into the IQ-TREE standard version once stable enough.

How to cite IQ-TREE?

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 (Minh et al. 2013) 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 tree reconstruction or other features please cite:

L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. 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

If you used partition models e.g., for phylogenomic analysis please cite:

O. Chernomor, A. von Haeseler, and B.Q. Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol., 65:997-1008.
DOI: 10.1093/sysbio/syw037

If you performed the ultrafast bootstrap (UFBoot) please cite:

B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultrafast approximation for phylogenetic bootstrap. Mol. Biol. Evol., 30:1188-1195.
DOI: 10.1093/molbev/mst024

If you used the polymorphism-aware models please cite:

D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, and C. Kosiol (2016) Reversible polymorphism-aware phylogenetic models and their application to tree inference. J. Theor. Biol., 407:362–370.
DOI: 10.1016/j.jtbi.2016.07.042

If you used the IQ-TREE web server please cite:

J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, and B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res., 44 (W1):W232-W235.
DOI: 10.1093/nar/gkw256