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IQ-TREE is free software that infers phylogenetic trees from aligned sequences by maximum likelihood. It selects a substitution model automatically, estimates branch support with ultrafast bootstrap, and can report concordance factors that show how much of a genome-scale dataset agrees with each branch. This page explains what it does, the minimal commands, how to read its support values, and how the versions and web servers differ.
Short answer
IQ-TREE reads a multiple sequence alignment, picks a model with ModelFinder, searches for the maximum-likelihood tree and writes the tree plus a text report. Its documentation lists automatic model selection, ultrafast bootstrap (UFBoot), gene and site concordance factors (gCF, sCF), partition and mixture models, and LSD2 and MCMCtree dating. A free web server is also hosted at CIBIV (Austria), Los Alamos (USA) and the CIPRES Gateway (USA).
What IQ-TREE does
IQ-TREE is a command-line program for maximum-likelihood phylogenetics. You supply an alignment, for example one produced with Clustal Omega and inspected in Jalview, and it returns a tree in Newick format. The IQ-TREE 2 paper (Minh et al., Molecular Biology and Evolution 2020; 37(5):1530-1534, doi 10.1093/molbev/msaa015) describes version 2 as adding non-time-reversible models for rooted trees, plus partitioned, mixture, heterotachy and polymorphism-aware models. IQ-TREE version 1 was released in 2014.
It is a maximum-likelihood tool. For parsimony analysis see PAUP*; for Bayesian sampling see Markov chain Monte Carlo. The broader workflow, including an IQ-TREE 2 command-line alternative, is in Make a Phylogenetic Tree: Software and Methods.
Running it: the minimal commands
The IQ-TREE tutorial starts from a single command: iqtree -s example.phy, where -s names the alignment file. From v1.5.4 the default is -m MFP (ModelFinder Plus), which chooses a model using BIC by default; -AIC and -AICc are alternatives. The tutorial recommends -T AUTO for choosing the number of CPU cores, with -ntmax to cap them.
Branch support is requested with -B (the number of ultrafast bootstrap replicates; the tutorial says 1000 is the minimum recommended) and -alrt 1000 for the SH-aLRT test. Using -alrt 1000 -B 1000 runs both. In version 1.x the ultrafast bootstrap option is -bb rather than -B.
Output files
.iqtree: the main report, including a text drawing of the tree..treefile: the maximum-likelihood tree in Newick format..log: the run log..cf.tree,.cf.branch,.cf.stat: concordance-factor outputs, described below.
Reading support values
This is where most misreadings happen. The IQ-TREE FAQ (page last updated 29 June 2024) gives these rules of thumb:
| Measure | What it is | What the documentation says |
|---|---|---|
| UFBoot | Ultrafast bootstrap support per branch | Rely on a branch only if support is at least 95%. Do not compare UFBoot percentages directly with standard bootstrap percentages. |
| SH-aLRT | Approximate likelihood-ratio test per branch | One is more confident if a clade has SH-aLRT of at least 80% and UFBoot of at least 95%. |
| gCF | Gene concordance factor | The percentage of decisive gene trees that contain the branch. |
| sCF | Site concordance factor | The percentage of decisive alignment sites that support the branch in the reference tree. |
For concatenated phylogenomic data, UFBoot and bootstrap values tend to reach 100%, so the 95% guidance does not apply there. The FAQ recommends computing concordance factors for any phylogenomic analysis. The concordance-factor page shows the gCF command as iqtree3 -t concat.treefile --gcf loci.treefile --prefix concord, which writes concord.cf.tree, concord.cf.branch and concord.cf.stat (gCF and gDF per branch). The sCF command is iqtree3 -te concat.treefile -s ALN_FILE --scfl 100 --prefix concord2; the likelihood-based --scfl needs version 2.2.2 or later, while older versions use the parsimony-based --scf.
For how to interpret a finished tree, see How to Read a Phylogenetic Tree.
Versions and web server
| Version | Command and option notes (from the IQ-TREE documentation) |
|---|---|
| 1.x | Command iqtree; ultrafast bootstrap is -bb; -m MFP default since 1.5.4. |
| 2.x | Ultrafast bootstrap is -B; --scfl from 2.2.2. |
| 3 | The current FAQ and concordance-factor examples use the iqtree3 command (separate iqtree3 repository on GitHub). |
Many online tutorials show older option names, so check which version produced the command you are copying. Release notes are on the documentation site. If you do not want a local install, the documentation lists a free web server at CIBIV, Los Alamos and the CIPRES Gateway.
Common misunderstandings
- “A UFBoot of 95% equals a bootstrap of 95%.” The FAQ says the two should not be compared directly.
- “High support means the gene trees agree.” For concatenated data, UFBoot and bootstrap tend toward 100%; concordance factors are the check on disagreement among genes and sites.
- “Any command from a tutorial will work.” Option names changed between versions, as shown above.
FAQ
Where is the IQ-TREE manual?
The documentation index at iqtree.github.io/doc/ covers the tutorial, FAQ, model selection, bootstrap, concordance factors and release notes.
Is there an IQ-TREE online version?
Yes. The documentation lists a free web server hosted at CIBIV (Austria), Los Alamos (USA) and the CIPRES Gateway (USA).
What are gene trees and gCF used for?
You infer one tree per locus, then compare them with the species tree. gCF reports, per branch, the percentage of decisive gene trees containing it.
Does IQ-TREE do dating?
The documentation index lists LSD2 and MCMCtree-based dating among its features; its dating pages hold the commands.
Sources
- IQ-TREE documentation index, tutorial, FAQ (updated 29 June 2024) and concordance-factor page, iqtree.github.io/doc/, read 2026-11-08.
- Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020;37(5):1530-1534. doi 10.1093/molbev/msaa015, PMC7182206.
