Maximum-likelihood tree inference
Run IQ-TREE phylogenetic tree inference
IQ-TREE estimates an evolutionary tree from aligned DNA or protein sequences using maximum likelihood. It is used when you have a sequence alignment and want a statistically supported phylogenetic tree. It takes one FASTA or Clustal alignment, with an optional partition file, and produces a tree file. It can select a suitable evolutionary model automatically and calculate branch support with UFBoot and SH-aLRT. Phylomena records the model, support settings, seed, command, input, and result for reproducibility.
Supported versions
| Version | Released | Implemented in Phylomena |
|---|---|---|
| 2.4.0 |
Citations
- 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.
- Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14(6):587-589. doi:10.1038/nmeth.4285.
- Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35(2):518-522. doi:10.1093/molbev/msx281.