IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

doi:10.1093/molbev/msaa015

. 2020 May 1;37(5):1530-1534.

doi: 10.1093/molbev/msaa015.

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh^{1

2}, Heiko A Schmidt³, Olga Chernomor³, Dominik Schrempf^{3

4}, Michael D Woodhams⁵, Arndt von Haeseler^{3

6}, Robert Lanfear²

Affiliations

¹ Research School of Computer Science, Australian National University, Canberra, ACT, Australia.
² Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia.
³ Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna, Austria.
⁴ Department of Biological Physics, Eötvös Lórand University, Budapest, Hungary.
⁵ Discipline of Mathematics, University of Tasmania, Hobart, TAS, Australia.
⁶ Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria.

PMID: 32011700
PMCID: PMC7182206
DOI: 10.1093/molbev/msaa015

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al. Mol Biol Evol. 2020.

. 2020 May 1;37(5):1530-1534.

doi: 10.1093/molbev/msaa015.

Authors

Bui Quang Minh^{1

2}, Heiko A Schmidt³, Olga Chernomor³, Dominik Schrempf^{3

4}, Michael D Woodhams⁵, Arndt von Haeseler^{3

6}, Robert Lanfear²

Affiliations

¹ Research School of Computer Science, Australian National University, Canberra, ACT, Australia.
² Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia.
³ Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna, Austria.
⁴ Department of Biological Physics, Eötvös Lórand University, Budapest, Hungary.
⁵ Discipline of Mathematics, University of Tasmania, Hobart, TAS, Australia.
⁶ Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria.

PMID: 32011700
PMCID: PMC7182206
DOI: 10.1093/molbev/msaa015

Erratum in

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. Minh BQ, et al. Mol Biol Evol. 2020 Aug 1;37(8):2461. doi: 10.1093/molbev/msaa131. Mol Biol Evol. 2020. PMID: 32556291 Free PMC article. No abstract available.

Abstract

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

Keywords: maximum likelihood; models of sequence evolution; phylogenetics; phylogenomics.

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References

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1. Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O.. 2011. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol. 60(5):685–699. - PMC - PubMed
1. Biczok R, Bozsoky P, Eisenmann P, Ernst J, Ribizel T, Scholz F, Trefzer A, Weber F, Hamann M, Stamatakis A.. 2018. Two C plus plus libraries for counting trees on a phylogenetic terrace. Bioinformatics 34:3399–3401. - PMC - PubMed
1. Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 37(8):852–857. - PMC - PubMed

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[1] Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Gruning BA, et al. 2018. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46(W1):W537–W544. - PMC - PubMed

[2] Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Gruning BA, et al. 2018. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res. 46(W1):W537–W544. - PMC - PubMed

[3] Anisimova M, Gascuel O.. 2006. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol. 55(4):539–552. - PubMed

[4] Anisimova M, Gascuel O.. 2006. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst Biol. 55(4):539–552. - PubMed

[5] Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O.. 2011. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol. 60(5):685–699. - PMC - PubMed

[6] Anisimova M, Gil M, Dufayard JF, Dessimoz C, Gascuel O.. 2011. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol. 60(5):685–699. - PMC - PubMed

[7] Biczok R, Bozsoky P, Eisenmann P, Ernst J, Ribizel T, Scholz F, Trefzer A, Weber F, Hamann M, Stamatakis A.. 2018. Two C plus plus libraries for counting trees on a phylogenetic terrace. Bioinformatics 34:3399–3401. - PMC - PubMed

[8] Biczok R, Bozsoky P, Eisenmann P, Ernst J, Ribizel T, Scholz F, Trefzer A, Weber F, Hamann M, Stamatakis A.. 2018. Two C plus plus libraries for counting trees on a phylogenetic terrace. Bioinformatics 34:3399–3401. - PMC - PubMed

[9] Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 37(8):852–857. - PMC - PubMed

[10] Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. 2019. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 37(8):852–857. - PMC - PubMed

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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

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