nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models
Author
Dang, Cuong CaoMinh, Bui Quang
McShea, Hanon
Masel, Joanna
James, Jennifer Eleanor
Vinh, Le Sy
Lanfear, Robert
Affiliation
Department of Ecology and Evolutionary Biology, University of ArizonaIssue Date
2022
Metadata
Show full item recordPublisher
Oxford University PressCitation
Dang, C. C., Minh, B. Q., McShea, H., Masel, J., James, J. E., Vinh, L. S., & Lanfear, R. (2022). nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models. Systematic Biology, 71(5), 1110–1123.Journal
Systematic biologyRights
© The Author(s) 2022. Published by Oxford University Press on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).Collection Information
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.Abstract
Amino acid substitution models are a key component in phylogenetic analyses of protein sequences. All commonly used amino acid models available to date are time-reversible, an assumption designed for computational convenience but not for biological reality. Another significant downside to time-reversible models is that they do not allow inference of rooted trees without outgroups. In this article, we introduce a maximum likelihood approach nQMaker, an extension of the recently published QMaker method, that allows the estimation of time nonreversible amino acid substitution models and rooted phylogenetic trees from a set of protein sequence alignments. We show that the nonreversible models estimated with nQMaker are a much better fit to empirical alignments than pre-existing reversible models, across a wide range of data sets including mammals, birds, plants, fungi, and other taxa, and that the improvements in model fit scale with the size of the data set. Notably, for the recently published plant and bird trees, these nonreversible models correctly recovered the commonly estimated root placements with very high-statistical support without the need to use an outgroup. We provide nQMaker as an easy-to-use feature in the IQ-TREE software (http://www.iqtree.org), allowing users to estimate nonreversible models and rooted phylogenies from their own protein data sets. The data sets and scripts used in this article are available at https://doi.org/10.5061/dryad.3tx95x6hx.Note
Open access articleEISSN
1076-836XPubMed ID
35139203Version
Final published versionAdditional Links
https://datadryad.org/stash/dataset/doi:10.5061/dryad.3tx95x6hxae974a485f413a2113503eed53cd6c53
10.1093/sysbio/syac007
Scopus Count
Collections
Except where otherwise noted, this item's license is described as © The Author(s) 2022. Published by Oxford University Press on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/).
Related articles
- QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution.
- Authors: Minh BQ, Dang CC, Vinh LS, Lanfear R
- Issue date: 2021 Aug 11
- Data-specific substitution models improve protein-based phylogenetics.
- Authors: Brazão JM, Foster PG, Cox CJ
- Issue date: 2023
- Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals.
- Authors: Naser-Khdour S, Quang Minh B, Lanfear R
- Issue date: 2022 Jun 16
- An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation.
- Authors: Wang HC, Susko E, Roger AJ
- Issue date: 2014 Apr
- Estimating amino acid substitution models from genome datasets: a simulation study on the performance of estimated models.
- Authors: Tinh NH, Dang CC, Vinh LS
- Issue date: 2024 Feb 14