The Vienna web server stops jobs requiring more than 24 hours or 1 GB of RAM.
Large analyses may need to be resumed locally or run on a separately provisioned machine.
Evidence source ↗
IQ-TREE
IQ-TREE infers phylogenetic trees from sequence alignments using maximum likelihood, with model selection and branch-support methods.
6 key claims verifiedOur editorial team checked this profile against vendor documentation, company information, product documentation. Supported by 4 documented sources.
Editorial overview
Aggregated Overview
The feature assessment reflects documented inference, model-selection, simulation, and support methods. Free GPL-licensed software scores strongly on license cost; command-line use adds setup effort. No reliable public review evidence was accessed, so user sentiment is unassessed.
This profile combines documented product information and independent evidence where available. It is not a hands-on test unless TechZella explicitly identifies one.
Overview
IQ-TREE is open-source software for inferring phylogenetic trees using maximum likelihood. The project has been developed since 2011 under the GNU GPL version 2.
Researchers can run the command-line program locally or submit alignments through a documented web server. The core workflow supports automatic model selection and branch-support analyses. The Vienna web server has stated resource limits, so larger jobs may require local or separately provisioned computing.
IQ-TREE Decision Snapshot
A quick way to understand who this product may suit, where its limits matter, and which facts are most relevant before you compare alternatives.
Best suited to
Researchers and bioinformatics teams that need local or web-based maximum-likelihood phylogenetic inference, model selection, and branch support analysis.
Look elsewhere if
Users who require a graphical desktop workflow, managed compute without job limits, or a general-purpose tree visualization application, and should evaluate alternatives such as RAxML-NG instead.
Platforms
CLI, Linux, macOS, Web, Windows
TechZella assessment
7.1/10
IQ-TREE — What Sets It Apart?
These are the product-specific differences that may matter when deciding whether the software fits your workflow. They are based on documented evidence rather than a universal ranking.
- Combines maximum-likelihood tree inference with ModelFinder model selection and ultrafast bootstrap support.
- Supports DNA, protein, codon, binary, and morphological data types, as well as partitioned and mixture analyses.
- The piqtree library exposes selected IQ-TREE capabilities through Python and cogent3.
IQ-TREE Pros & Cons
Pros
- Freely available under GNU GPL version 2.
- Includes automatic model selection and multiple branch-support methods.
- Provides native Windows, macOS, and Linux downloads.
- Offers both command-line execution and a web-server workflow.
Cons
- The primary application requires command-line use.
- The documented Vienna web server has CPU-time and memory limits.
- Local analyses require users to arrange their own compute resources.
IQ-TREE Gotchas & Operational Limits
These are documented constraints or practical friction points that may matter before you adopt the product.
The command-line application must be run from a terminal or console.
Users expecting a native graphical desktop application may need training or a separate analysis interface.
Evidence source ↗IQ-TREE Pricing & Plans
Free open-source software
$0
not applicable
Freely available under GNU GPL version 2. Local computing resources are provided separately by the user.
Check current pricing →Pricing may change. Verify current plans on the vendor's website.
IQ-TREE Competitors & Alternatives
Compare similar products directly, then see which alternatives may make more sense when your requirements differ.
At a glance
Open Source Software| Decision factor | IQ-TREE | RAxML-NG |
|---|---|---|
| Core scope | Maximum-likelihood phylogenetic inference with integrated model selection, ultrafast bootstrap, and other analysis methods. | Maximum-likelihood phylogenetic inference with adaptive search heuristics, automatic model selection, and branch-support metrics. Source ↗ |
| License | GNU GPL version 2. | GNU AGPL version 3. Source ↗ |
| Platform and installation | Native 64-bit Windows, macOS, and Linux downloads; command-line use. | Precompiled Linux and macOS binaries; Windows users can use the Linux binary through WSL. Source ↗ |
| Programmatic access | Command-line application plus the piqtree Python library interface. | Command-line application with build-from-source options, including MPI. Source ↗ |
Only factors supported by the available research are shown. The comparison is descriptive, not a ranking.
Direct competitors
These products address broadly similar requirements. The descriptions focus on documented reasons a buyer might compare them with IQ-TREE.
RAxML-NGMaximum-likelihood phylogenetic inference with adaptive search heuristics, automatic model selection, and branch-support metrics.
IQ-TREE Features
Phylogenetic inference
- Maximum-likelihood tree inference
- Tree topology searches
- Partitioned and mixture models
Modeling and support
- ModelFinder automatic model selection
- Ultrafast bootstrap
- Branch tests and concordance factors
Additional analysis
- AliSim sequence simulation
- Phylogenetic dating
- Ancestral sequence reconstruction
Interfaces and ecosystem
- Command-line application
- Web server for tree inference and model selection
- piqtree Python library using cogent3
Demo & Screenshots
IQ-TREE Specifications
| License | GNU GPL version 2 |
|---|---|
| Native operating systems | Windows, macOS, Linux |
| Primary interface | Command line |
| Web interface | Online inference and model-selection server |
| Data types | DNA, protein, codon, binary, morphological |
| Python interface | piqtree library; cogent3 interface |
| Free trial | Not applicable; software is freely available |
| Web server resource limits | Documented Vienna server: 24 hours CPU time and 1 GB RAM |
Deployment & System Footprint
Verified installation, hosting, administration, or environment details that can affect implementation.
| Installation or hosting | Download native Windows, macOS, or Linux builds for local command-line execution; an online web server is also documented. Source ↗ |
|---|---|
| License | Open-source software under GNU GPL version 2. Source ↗ |
Our evidence-based assessment
TechZella Score
A proprietary editorial score based on product capabilities, usability, value, performance, support and user sentiment evidence.
7.1/10Moderate confidence
The feature assessment reflects documented inference, model-selection, simulation, and support methods. Free GPL-licensed software scores strongly on license cost; command-line use adds setup effort. No reliable public review evidence was accessed, so user sentiment is unassessed.
Methodology v1.0. The assessment weighs feature coverage (25%), ease of use (15%), value for money (20%), performance (15%), support (10%) and user sentiment (15%), using researched product evidence and verified review evidence where available. It is a TechZella editorial assessment, not a direct user-review average.
Editorial transparency
Our Review Methodology
Key claims are linked to the sources used to verify them. This evidence record is separate from third-party user ratings.
TechZella evaluates software using documented product capabilities, pricing information, usability and value considerations, independent user evidence where available, and competitive context. The assessment is an editorial review, not a hands-on test unless one is explicitly identified. Our editorial assessment is based on 4 documented sources.
What TechZella adds
- Combines maximum-likelihood tree inference with ModelFinder model selection and ultrafast bootstrap support.
- Supports DNA, protein, codon, binary, and morphological data types, as well as partitioned and mixture analyses.
- The piqtree library exposes selected IQ-TREE capabilities through Python and cogent3.
Important limitations
- The main downloadable application is command-line software, so users need terminal familiarity.
- The documented Vienna web server stops jobs exceeding 24 hours or 1 GB RAM; larger jobs need local execution or another compute environment.
Evidence-backed claimsIQ-TREE has been developed since 2011 and is open source. The current listed release is IQ-TREE 3.1.4, dated September 10, 2026. IQ-TREE offers native downloads for Windows, macOS, and Linux. The Vienna web server supports tree inference and model selection from alignment uploads. The documented Vienna web server stops jobs exceeding 24 hours or 1 GB RAM. The piqtree library provides a Python interface to selected IQ-TREE functions.
The project page gives 2011 as the development start and identifies the GNU GPL license.
View source ↗Verified 2026-11-10The official download page identifies version 3.1.4 and its release date.
View source ↗Verified 2026-11-10The official download page lists 64-bit builds for all three operating systems.
View source ↗Verified 2026-11-10The web server tutorial documents both workflows and supported alignment file formats.
View source ↗Verified 2026-11-10The web server tutorial states these resource thresholds and describes resuming stopped jobs locally.
View source ↗Verified 2026-11-10The project's piqtree repository describes the Python library and examples for tree construction and model selection.
View source ↗Verified 2026-11-10IQ-TREE FAQs
Answers begin with the clearest available response, followed by the context that helps you act on it.
Is IQ-TREE free?
Yes. The project describes it as freely available open-source software under GNU GPL version 2.
Does IQ-TREE run on Windows?
Yes. The official download page lists a 64-bit Windows version.
Can I use IQ-TREE from Python?
Yes. The separate piqtree library exposes selected IQ-TREE features through Python and cogent3.
What are the IQ-TREE web server limits?
The documented Vienna server stops jobs that require more than 24 hours or 1 GB RAM; stopped work can be resumed locally from a checkpoint.
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