IQ-TREE

IQ-TREE is a software package for phylogenetic inference, including tree reconstruction, model selection, bootstrap approximation (UFBoot), and big data analysis. The IQ-TREE algorithm includes various evolutionary models, such as mixture, partition, and common substitution.

Topic

Phylogenetics;Statistics and probability;Phylogenomics

Detail

  • Operation: Phylogenetic tree generation (maximum likelihood and Bayesian methods)

  • Software interface: Command-line user interface

  • Language: C++, Python

  • License: GNU General Public License v2

  • Cost: Free

  • Version name: 2.2.0. stable: 1.6.12

  • Credit: Universität Wien, FWF Der Wissenschaftsfond, Australian National University, Australian Government, Chan Zuckerberg Initiative, Simons Foundation, Gordon and Betty Moore Foundation.

  • Input: -

  • Output: -

  • Contact: admin.vbc5@univie.ac.at

  • Collection: IQ-TREE

  • Maturity: Mature

Publications

  • Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity
  • Schrempf D, Minh BQ, von Haeseler A, Kosiol C. Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity. Mol Biol Evol. 2019 Jun 1;36(6):1294-1301. doi: 10.1093/molbev/msz043. PMID: 30825307; PMCID: PMC6526911.
  • https://doi.org/0.1093/molbev/msz043
  • PMID: 30825307
  • PMC: PMC6526911
  • ModelFinder: fast model selection for accurate phylogenetic estimates
  • Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017 Jun;14(6):587-589. doi: 10.1038/nmeth.4285. Epub 2017 May 8. PMID: 28481363; PMCID: PMC5453245.
  • https://doi.org/10.1038/nmeth.4285
  • PMID: 28481363
  • PMC: PMC5453245
  • IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era
  • 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 May 1;37(5):1530-1534. doi: 10.1093/molbev/msaa015. Erratum in: Mol Biol Evol. 2020 Aug 1;37(8):2461. PMID: 32011700; PMCID: PMC7182206.
  • https://doi.org/10.1093/molbev/msaa015
  • PMID: 32011700
  • PMC: PMC7182206
  • New Methods to Calculate Concordance Factors for Phylogenomic Datasets
  • Minh BQ, Hahn MW, Lanfear R. New Methods to Calculate Concordance Factors for Phylogenomic Datasets. Mol Biol Evol. 2020 Sep 1;37(9):2727-2733. doi: 10.1093/molbev/msaa106. PMID: 32365179; PMCID: PMC7475031.
  • https://doi.org/10.1093/molbev/msaa106
  • PMID: 32365179
  • PMC: PMC7475031
  • Corrigendum to: IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
  • Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R. Corrigendum to: IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol Biol Evol. 2020 Aug 1;37(8):2461. doi: 10.1093/molbev/msaa131. Erratum for: Mol Biol Evol. 2020 May 1;37(5):1530-1534. PMID: 32556291; PMCID: PMC7403609.
  • https://doi.org/10.1093/molbev/msaa131
  • PMID: 32556291
  • PMC: PMC7403609
  • IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
  • Nguyen LT, et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. 2015; 32:268-74. doi: 10.1093/molbev/msu300
  • https://doi.org/10.1093/molbev/msu300
  • PMID: 25371430
  • PMC: PMC4271533
  • Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
  • Chernomor O, von Haeseler A, Minh BQ. Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. Syst Biol. 2016 Nov;65(6):997-1008. doi: 10.1093/sysbio/syw037. Epub 2016 Apr 26. PMID: 27121966; PMCID: PMC5066062.
  • https://doi.org/10.1093/sysbio/syw037
  • PMID: 27121966
  • PMC: PMC5066062
  • Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation
  • Wang HC, Minh BQ, Susko E, Roger AJ. Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation. Syst Biol. 2018 Mar 1;67(2):216-235. doi: 10.1093/sysbio/syx068. PMID: 28950365.
  • https://doi.org/10.1093/sysbio/syx068
  • PMID: 28950365
  • PMC: -
  • GHOST: Recovering historical signal from heterotachously-evolved sequence alignments.
  • Crotty SM, Minh BQ, Bean NG, Holland BR, Tuke J, Jermiin LS, Haeseler AV. GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments. Syst Biol. 2020 Mar 1;69(2):249-264. doi: 10.1093/sysbio/syz051. PMID: 31364711.
  • https://doi.org/10.1093/sysbio/syz051
  • PMID: 31364711
  • PMC: -

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