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ModelFinder: fast model selection for accurate phylogenetic estimates

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Abstract

Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.

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Figure 1: ModelFinder obtains accurate phylogenetic estimates.
Figure 2: Advantages provided by ModelFinder.

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Acknowledgements

We thank D.Y. Wu, J.A. Eisen, P. Donoghue and A. Rokas for access to their data; E. Susko for discussions about the EM algorithm; and V. Jayaswal for constructive feedback. B.Q.M. and A.v.H. were supported by the Austrian Science Fund (FWF I-2805-B29).

Author information

Author notes

  1. Subha Kalyaanamoorthy, Bui Quang Minh and Thomas K F Wong: These authors contributed equally to this work.

Authors and Affiliations

  1. Land & Water, CSIRO, Canberra, Australian Capital Territory, Australia

    Subha Kalyaanamoorthy, Thomas K F Wong & Lars S Jermiin

  2. Faculty of Pharmacy & Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada

    Subha Kalyaanamoorthy

  3. Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna & Medical University of Vienna, Vienna, Austria

    Bui Quang Minh & Arndt von Haeseler

  4. Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia

    Thomas K F Wong & Lars S Jermiin

  5. Bioinformatics and Computational Biology, Faculty of Computational Science, University of Vienna, Vienna, Austria

    Arndt von Haeseler

Authors
  1. Subha Kalyaanamoorthy
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  2. Bui Quang Minh
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  3. Thomas K F Wong
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  4. Arndt von Haeseler
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  5. Lars S Jermiin
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Contributions

S.K., T.K.F.W. and L.S.J. conceived the method and executed a pilot study to assess the method's likely impact on model selection. B.Q.M. and T.K.F.W. implemented the method in IQ-TREE with contributions from S.K., L.S.J. and A.v.H. S.K., T.K.F.W., L.S.J. and B.Q.M. assessed the performance and accuracy of the method. S.K., T.K.F.W. and L.S.J. carried out the analyses of simulated and real data. L.S.J., S.K., T.K.F.W., B.Q.M. and A.v.H. wrote the paper.

Corresponding author

Correspondence to Lars S Jermiin.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Table 2 (PDF 298 kb)

Supplementary Table 1 (XLSX 54 kb)

Supplementary Software

IQ-TREE-1.4.2.tar.gz (ZIP 4685 kb)

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Kalyaanamoorthy, S., Minh, B., Wong, T. et al. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14, 587–589 (2017). https://doi.org/10.1038/nmeth.4285

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  • DOI: https://doi.org/10.1038/nmeth.4285

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