| name | iqtree |
| description | IQ-TREE 2 — fast maximum-likelihood phylogenetic inference with model selection and ultrafast bootstrap. Use when: (1) Building publication-grade trees from marker or concatenated MSAs, (2) Following PhyloPhlAn / custom alignments for MAG phylogenomics, (3) Replacing draft FastTree topologies for final figures. Upstream: https://github.com/iqtree/iqtree2. Route via phylogenomics.
|
| license | MIT |
| category | analysis-tools |
| tags | ["IQ-TREE","phylogeny","maximum-likelihood","tree","bootstrap"] |
| upstream | https://github.com/iqtree/iqtree2 |
| stage | taxonomy |
IQ-TREE 2
Upstream: iqtree/iqtree2 · http://www.iqtree.org
Citation
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic
inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
https://doi.org/10.1093/molbev/msaa015
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast
and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Mol. Biol. Evol. 32, 268–274 (2015). https://doi.org/10.1093/molbev/msu300
See also docs/references.md.
Analytical thinking
Default ML tree engine for metagenomic phylogenomics after you have a
clean MSA (from phylophlan, marker genes, or curated orthologs). ModelFinder
chooses substitution models; UFBoot gives rapid support values — report both
model and support method.
| vs | Prefer IQ-TREE when |
|---|
fasttree | Final / publication trees |
gtdbtk | You need a custom tree, not only GTDB placement |
lucaphylo | MSA-based classical phylogeny is appropriate |
Garbage in → garbage trees: remove poor MAGs, dubious alignments, and
outgroup contamination first.
How to run
iqtree2 -s markers.fa -m MFP -B 1000 -T AUTO -prefix temp/iqtree/run
Key parameters
| Setting | Notes |
|---|
-m MFP | ModelFinder Plus — state selected model |
-B 1000 | Ultrafast bootstrap replicates |
-T | Threads |
| Partition models | Use when concatenating heterogeneous markers |
Decision tree
Need a sequence-based tree?
├─ Draft / exploratory large MSA → fasttree
├─ Publication ML tree → iqtree
├─ Genome set workflow → phylophlan (± iqtree backend)
└─ MSA impossible / extreme divergence → lucaphylo
Related skills
phylogenomics · fasttree · phylophlan · gtdbtk · lucaphylo ·
mag-qc · tool-selection
