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---
layout: default
title: "IQ-TREE: Efficient phylogenomic software by maximum likelihood"
permalink: /
version: 2.4.0
version_new: 3.0.0
releasedate: February 7, 2025
releasedate_new: April 3, 2025
v1_url: https://github.com/iqtree/iqtree2/releases/download
v2_url: https://github.com/iqtree/iqtree3/releases/download
---
<!-- ========================== HEADER ========================== -->
<div id="headerwrap">
<div class="container">
<div class="row">
<div class="col-lg-8 col-lg-offset-2">
<h1><img src="assets/img/iqtree-logo.svg" width="200"> IQ-TREE</h1>
<h3>Efficient software for phylogenomic inference</h3>
<h3>Latest release {{page.version_new}} ({{page.releasedate_new}})</h3>
<p>
<a id="downloadwin_new" style="display: none;" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Windows.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version_new}} for Windows</a>
<a id="downloadmac_new" style="display: none;" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-macOS.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version_new}} for macOS Universal</a>
<a id="downloadlinux_new" style="display: none;" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Linux-intel.tar.gz" class="btn btn-danger btn-lg" role="button">Download v{{page.version_new}} for Linux Intel</a>
<a id="downloadlinux_new2" style="display: none;" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Linux-arm.tar.gz" class="btn btn-danger btn-lg" role="button">Download v{{page.version_new}} for Linux ARM</a>
</p>
<h3>Legacy release {{page.version}} ({{page.releasedate}})</h3>
<p>
<a id="downloadwin" style="display: none;" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Windows.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version}} for Windows</a>
<a id="downloadmac" style="display: none;" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-macOS.zip" class="btn btn-danger btn-lg" role="button">Download v{{page.version}} for macOS</a>
<a id="downloadlinux" style="display: none;" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Linux-intel.tar.gz" class="btn btn-danger btn-lg" role="button">Download v{{page.version}} for Linux Intel</a>
</p>
<p>
<a id="downloadall" href="#download" class="btn btn-primary btn-lg" role="button">All Downloads</a>
<a href="doc/" class="btn btn-primary btn-lg" role="button">Documentation</a>
</p>
</div>
</div><!-- /row -->
</div> <!-- /container -->
</div> <!-- /headerwrap -->
<script type="text/javascript">
function getOS() {
var userAgent = window.navigator.userAgent,
platform = window.navigator.platform,
macosPlatforms = ['Macintosh', 'MacIntel', 'MacPPC', 'Mac68K'],
windowsPlatforms = ['Win32', 'Win64', 'Windows', 'WinCE'],
iosPlatforms = ['iPhone', 'iPad', 'iPod'],
os = null;
if (macosPlatforms.indexOf(platform) !== -1) {
os = 'macOS';
} else if (iosPlatforms.indexOf(platform) !== -1) {
os = 'iOS';
} else if (windowsPlatforms.indexOf(platform) !== -1) {
os = 'Windows';
} else if (/Android/.test(userAgent)) {
os = 'Android';
} else if (!os && /Linux/.test(platform)) {
os = 'Linux';
}
return os;
}
var os = getOS();
if (os == "Windows") {
document.getElementById("downloadwin").style.display = "inline";
document.getElementById("downloadwin_new").style.display = "inline";
} else if (os == "macOS") {
document.getElementById("downloadmac").style.display = "inline";
document.getElementById("downloadmac_new").style.display = "inline";
} else if (os == "Linux") {
document.getElementById("downloadlinux").style.display = "inline";
document.getElementById("downloadlinux_new").style.display = "inline";
document.getElementById("downloadlinux_new2").style.display = "inline";
} else document.getElementById("downloadall").innerHTML="Download";
</script>
<!-- ========================== IQ-TREE key features ========================== -->
<div class="service container">
<div class="row centered">
<div class="col-sm-12">
<br><h3>IQ-TREE feature highlights</h3>
</div>
<div class="col-sm-6">
<i class="fa fa-usb fa-rotate-270"></i>
<h4>IQ-TREE - Efficient Tree Reconstruction</h4>
<p>A fast search algorithm (<a href="http://dx.doi.org/10.1093/molbev/msu300">Nguyen et al., 2015</a>)
to infer phylogenetic trees by maximum likelihood.
IQ-TREE compares favorably to RAxML and PhyML.</p>
</div>
<div class="col-sm-6">
<i class="fa fa-user-md"></i>
<h4>ModelFinder - Fast and Accurate Model Selection</h4>
<p>ModelFinder (<a href="http://dx.doi.org/10.1038/nmeth.4285">Kalyaanamoorthy et al., 2017</a>)
is <em>10 to 100 times faster than jModelTest and ProtTest</em>. It also finds best-fit
partitioning scheme like <a href="http://www.robertlanfear.com/partitionfinder/">PartitionFinder</a>.</p>
</div>
</div>
<div class="row centered">
<div class="col-sm-6">
<i class="fa fa-fighter-jet"></i>
<h4>UFBoot - Ultrafast Bootstrap Approximation</h4>
<p>UFBoot (<a href="http://dx.doi.org/10.1093/molbev/mst024">Minh et al., 2013</a>)
provides approximately unbiased branch support values and runs 100X faster than
nonparametric bootstrap and 10 to 40 times faster than RAxML rapid bootstrap.</p>
</div>
<div class="col-sm-6">
<i class="fa fa-tasks"></i>
<h4>AliSim - Alignment Simulator <span class="label label-danger"><em>New!</em></span></h4>
<p>AliSim (<a href="https://doi.org/10.1093/bioinformatics/btad540">Ly-Trong et al., 2023</a>) allows to
quickly <a href="doc/AliSim">simulate multiple sequence alignments</a> under more realistic models than Seq-Gen and INDELible.
</p>
</div>
</div>
<br>
<div class="row">
<div class="col-md-10 col-md-offset-1 col-lg-8 col-lg-offset-2">
<div class="list-group">
<div class="list-group-item list-group-item-warning">
<h4 class="centered">Version 2.0 Highlights</h4>
<ul>
<li>Supporting large datasets with <a href="doc/Command-Reference#checkpointing-to-resume-stopped-run">checkpointing</a>,
<a href="doc/Command-Reference#general-options">safe numerical and low memory mode</a></li>
<li>High performance computing with <a href="doc/Tutorial#utilizing-multi-core-cpus">Multicore CPUs</a>
and <a href="doc/Compilation-Guide#compiling-mpi-version">distributed MPI system</a></li>
<li>Input alignment or partition can be a directory of alignment files</li>
<li>Inference of <a href="doc/Rootstrap">rooted trees</a> using non-reversible models</li>
<li>Faster tree search under <a href="doc/Advanced-Tutorial#constrained-tree-search">topological constraint</a></li>
<li>Gene/locus trees inference and <a href="doc/Concordance-Factor">concordance factor analysis</a></li>
<li><a href="https://doi.org/10.1093/sysbio/syu062">ModelOMatic model selection</a> between DNA, protein and codon models (--modelomatic option)</li>
<li><a href="doc/Assessing-Phylogenetic-Assumptions">Tests of model violations</a></li>
<li><a href="doc/Advanced-Tutorial#inferring-site-specific-rates">Site rate estimation</a> by maximum likelihood</li>
<li><span class="label label-danger"><em>New!</em></span> Version 2.3.X supports macOS M1-3 (ARM) chips and new <a href="doc/Complex-Models">mixture models</a> (25 March 2024)</li>
</ul>
</div>
</div>
</div>
</div>
</div><!--/container -->
<br><div class="hline"></div><br>
<!-- ========================== IQ-TREE supports a wide range of evolutionary models ========================== -->
<div class="service container">
<div class="row centered">
<div class="col-sm-12">
<h3>IQ-TREE supports a wide range of evolutionary models</h3>
</div>
<div class="col-sm-4">
<i class="fa fa-retweet"></i>
<h4>Common Models</h4>
<p>All <a href="doc/Substitution-Models">common substitution models</a> for DNA, protein, codon, binary and morphological data with <a href="doc/Substitution-Models#rate-heterogeneity-across-sites">rate heterogeneity among sites</a>.</p>
</div>
<div class="col-sm-4">
<i class="fa fa-pie-chart"></i>
<h4>Partition Models</h4>
<p><a href="doc/Complex-Models">Phylogenomic partition models</a> allowing for mixed data types, mixed rate heterogeneity types, linked or unlinked branch lengths.</p>
</div>
<div class="col-sm-4">
<i class="fa fa-flask"></i>
<h4>Mixture Models</h4>
<p>Mixture models such as <a href="doc/Substitution-Models#protein-mixture-models">empirical protein mixture models</a> and <a href="doc/Complex-Models#mixture-models">customizable mixture models</a>.</p>
</div>
</div>
</div><!--/container -->
<br><div class="hline"></div><br>
<!-- ========================== IQ-TREE is user-friendly and well-documented ========================== -->
<div class="service container">
<div class="row centered">
<div class="col-sm-12">
<h3>IQ-TREE is user-friendly and well-documented</h3>
</div>
<div class="col-sm-4">
<i class="fa fa-globe"></i>
<h4>Online Web Service</h4>
Easy to use web servers provided by:<br>
<a href="http://iqtree.cibiv.univie.ac.at" target="_blank">Center for Integrative Bioinformatics Vienna, Austria</a><br>
<a href="https://www.hiv.lanl.gov/content/sequence/IQTREE/iqtree.html" target="_blank">Los Alamos National Laboratory, USA</a>
</div>
<div class="col-sm-4">
<i class="fa fa-question-circle"></i>
<h4>User Support</h4>
Please refer to <a href="doc/Frequently-Asked-Questions">Frequently Asked Questions</a>.
For further questions and feedback, please create a new topic on
<a href="https://github.com/iqtree/iqtree2/discussions">IQ-TREE GitHub discussions</a> <span class="label label-danger"><em>New!</em></span>
</div>
<div class="col-sm-4">
<a href="doc/">
<i class="fa fa-book"></i>
<h4>User Documentation</h4>
</a>
User guide, tutorial and extensive documentation for how to use IQ-TREE.
</div>
</div><!--row-->
</div> <!-- /container -->
<!-- ========================== DOWNLOAD ========================== -->
<div id="download" class="service jumbotron">
<div class="container">
<div class="row centered">
<div class="col-sm-12">
<h2>Download</h2>
</div>
<div class="col-sm-12">
<p>Latest release {{page.version_new}} ({{page.releasedate_new}})</p>
</div>
<div class="col-sm-4">
<i class="fa fa-windows"></i>
<h4>Windows</h4>
<div class="list-group">
<a class="list-group-item list-group-item-info" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Windows.zip">64-bit Windows</a>
</div>
</div>
<div class="col-sm-4">
<i class="fa fa-apple"></i>
<h4>macOS</h4>
<div class="list-group">
<a class="list-group-item list-group-item-info" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-macOS.zip">64-bit macOS Universal</a>
<a class="list-group-item list-group-item-success" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-macOS-intel.zip">64-bit macOS Intel</a>
<a class="list-group-item list-group-item-info" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-macOS-arm.zip">64-bit macOS Apple M chip (ARM)</a>
</div>
</div>
<div class="col-sm-4">
<i class="fa fa-linux"></i>
<h4>Linux</h4>
<div class="list-group">
<a class="list-group-item list-group-item-info" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Linux-intel.tar.gz">64-bit Linux Intel</a>
<a class="list-group-item list-group-item-success" href="{{page.v2_url}}/v{{page.version_new}}/iqtree-{{page.version_new}}-Linux-arm.tar.gz">64-bit Linux ARM</a>
</div>
</div>
<div class="col-sm-12">
<p>IQ-TREE version {{page.version}} ({{page.releasedate}})</p>
</div>
<div class="col-sm-4">
<div class="list-group">
<a class="list-group-item list-group-item-info" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Windows.zip">64-bit Windows</a>
</div>
</div>
<div class="col-sm-4">
<div class="list-group">
<a class="list-group-item list-group-item-info" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-macOS.zip">64-bit macOS Universal</a>
<a class="list-group-item list-group-item-success" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-macOS-intel.zip">64-bit macOS Intel</a>
<a class="list-group-item list-group-item-info" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-macOS-arm.zip">64-bit macOS Apple M chip (ARM)</a>
</div>
</div>
<div class="col-sm-4">
<div class="list-group">
<a class="list-group-item list-group-item-info" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Linux-intel.tar.gz">64-bit Linux Intel</a>
<a class="list-group-item list-group-item-success" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-Linux-arm.tar.gz">64-bit Linux ARM</a>
<!--<a class="list-group-item list-group-item-info" href="{{page.v1_url}}/v{{page.version}}/iqtree-{{page.version}}-LinuxKNL.tar.gz">Xeon Phi Knights Landing Linux</a>-->
</div>
</div>
</div> <!-- row -->
<div class="row">
<div class="col-sm-4">
<div class="list-group">
<a href="doc/Quickstart" class="list-group-item">
<div class="list-group-item-text"><h4>Getting started</h4>Beginner's guide for a quick start.</div>
</a>
</div>
</div>
<div class="col-sm-4">
<div class="list-group">
<a href="release/" class="list-group-item">
<div class="list-group-item-text"><h4>Version 1</h4>Downloads and release notes of IQ-TREE 1.</div>
</a>
</div>
</div>
<div class="col-sm-4">
<div class="list-group">
<a href="doc/Compilation-Guide" class="list-group-item">
<div class="list-group-item-text"><h4>Compilation guide</h4>Building IQ-TREE from source code.</div>
</a>
</div>
</div>
</div><!-- /row -->
</div> <!-- /container -->
</div><!-- /jumbotron -->
<!-- ========================== How to cite IQ-TREE? ========================== -->
<script type='text/javascript' src='https://d1bxh8uas1mnw7.cloudfront.net/assets/embed.js'></script>
<div class="service container">
<div class="row">
<div class="col-md-10 col-md-offset-1 col-lg-8 col-lg-offset-2">
<br><h2 class="centered">How to cite?</h2>
<div class="list-group">
<div class="list-group-item list-group-item-danger">
To maintain IQ-TREE, support users and obtain fundings,
it is important that you not only cite the IQ-TREE version 2 paper
(<a href="https://doi.org/10.1093/molbev/msaa015">Minh et al., 2020</a>)
but also additional papers typically mentioned in the documentation
of the features/options you are using in your analysis.
These papers are also <a href="doc/Home#how-to-cite-iq-tree">listed here</a>.
</div>
</div>
</div>
</div>
<div class="row">
<div class="col-md-12">
<h3 class="centered">IQ-TREE would not be possible without generous fundings by:</h3><br>
</div>
</div>
<div class="row">
<div class="col-sm-4">
<p class="centered">
<a href="https://www.univie.ac.at"><img src="assets/img/funding/univie-logo.jpg" width="200"></a>
</p>
</div>
<div class="col-sm-4">
<p class="centered">
<a href="https://fwf.ac.at"><img src="assets/img/funding/fwf-logo.jpg" width="200"></a>
</p>
</div>
<div class="col-sm-4">
<p class="centered">
<a href="https://www.anu.edu.au"><img src="assets/img/funding/anu-logo.png" width="200"></a>
</p>
</div>
</div>
<div class="row">
<div class="col-sm-4">
<p class="centered">
<a href="https://www.anu.edu.au"><img src="assets/img/funding/arc-logo.jpg" width="200"></a>
</p>
</div>
<div class="col-sm-4">
<p class="centered">
<a href="https://chanzuckerberg.com"><img src="assets/img/funding/czi-logo.svg" width="200"></a>
</p>
</div>
<div class="col-sm-4">
<p class="centered">
<a href="https://chanzuckerberg.com"><img src="assets/img/funding/simons-moore.jpg" width="200"></a>
</p>
</div>
</div>
</div><!--/container -->