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nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.

Cuong Cao Dang1, Bui Quang Minh2, Hanon McShea3

  • 1Faculty of Information Technology, University of Engineering and Technology, Vietnam National University, 144 Xuan Thuy, Cau Giay, Hanoi 10000, Vietnam.

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|February 9, 2022
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Summary
This summary is machine-generated.

Introducing nQMaker, a new method for estimating nonreversible amino acid substitution models and rooted phylogenetic trees. This approach offers a better fit to empirical data and accurately identifies root placements without outgroups.

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Area of Science:

  • Phylogenetics and evolutionary biology
  • Computational biology and bioinformatics

Background:

  • Amino acid substitution models are crucial for phylogenetic analysis of protein sequences.
  • Current models are time-reversible for computational ease, but this is biologically unrealistic and hinders rooted tree inference without outgroups.

Purpose of the Study:

  • To introduce nQMaker, a maximum likelihood method for estimating time nonreversible amino acid substitution models.
  • To enable the inference of rooted phylogenetic trees using these nonreversible models.
  • To improve the accuracy and biological realism of phylogenetic analyses.

Main Methods:

  • Developed nQMaker, an extension of the QMaker method, for maximum likelihood estimation of nonreversible amino acid substitution models.
  • Applied nQMaker to diverse empirical protein sequence alignments from various taxa (mammals, birds, plants, fungi).
  • Integrated nQMaker into the IQ-TREE software for user accessibility.

Main Results:

  • Nonreversible models estimated by nQMaker provide a significantly better fit to empirical alignments compared to existing reversible models.
  • Model fit improvement scales with the size of the data set.
  • nQMaker successfully recovered established root placements for plant and bird trees with high statistical support, eliminating the need for outgroups.

Conclusions:

  • nQMaker offers a more biologically realistic and computationally efficient approach to phylogenetic inference.
  • The ability to estimate nonreversible models and infer rooted trees without outgroups represents a significant advancement in phylogenetic analysis.
  • nQMaker is now available in IQ-TREE, empowering researchers to conduct more accurate protein sequence analyses.