ArticleSystematic biology2022
nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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22 citing papers in PubMed.
- Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages.Nature communications · 2026Article
- Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models.Molecular biology and evolution · 2026Article
- Mapping the absorption landscape of far-red Photosystem II.Nature communications · 2026Article
- Article
- IQ-TREE 3: phylogenomic inference software using complex evolutionary models.Molecular biology and evolution · 2026Article
- Identification of a distinct family of polyphosphate kinases relevant to energy homeostasis in Crenarchaeota.The Journal of biological chemistry · 2026Article
- Computational Analysis of Telomerase RNA Evolution inNon-coding RNA · 2026Article
- Reduced Amino Acid Substitution Matrices Find Traces of Ancient Coding Alphabets in Modern Day Proteins.Molecular biology and evolution · 2025Article
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- The effectiveness of selection in a species affects the direction of amino acid frequency evolution.bioRxiv : the preprint server for biology · 2025Article
- Horizontal Transfer of Bacterial Operons into Eukaryote Genomes.Genome biology and evolution · 2025Article
- Amino Acid Properties, Substitution Rates, and the Nearly Neutral Theory.Genome biology and evolution · 2025Article
- nT4X and nT4M: Novel Time Non-reversible Mixture Amino Acid Substitution Models.Journal of molecular evolution · 2025Article
- Order of amino acid recruitment into the genetic code resolved by last universal common ancestor's protein domains.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Genome assembly of a nocturnal butterfly (Macrosoma leucophasiata) reveals convergent adaptation of visual genes.Communications biology · 2024Article
- Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor's protein domains.bioRxiv : the preprint server for biology · 2024Article
- Reliable estimation of tree branch lengths using deep neural networks.PLoS computational biology · 2024Article
- CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era.Molecular biology and evolution · 2024Article
- Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction.Life (Basel, Switzerland) · 2024Review
- Ultrafast classical phylogenetic method beats large protein language models on variant effect prediction.Advances in neural information processing systems · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
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. [amino acid sequence analyses; amino acid substitution models; maximum likelihood model estimation; nonreversible models; phylogenetic inference; reversible models.].
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