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QMaker: Fast and accurate method to estimate empirical models of protein evolution.

ABSTRACT: Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models, however, they are typically complicated and slow. In this paper, we propose QMaker, a new ML method to estimate a general time-reversible Q matrix from a large protein dataset consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterogeneity among alignments, and the consideration of rate mixture models among sites. We provide QMaker as a user-friendly function in the IQ-TREE software package (http://www.iqtree.org) supporting the use of multiple CPU cores so that biologists can easily estimate amino acid substitution models from their own protein alignments. We used QMaker to estimate new empirical general amino acid substitution models from the current Pfam database as well as five clade-specific models for mammals, birds, insects, yeasts, and plants. Our results show that the new models considerably improve the fit between model and data and in some cases influence the inference of phylogenetic tree topologies.

SUBMITTER: Quang Minh B

PROVIDER: S-EPMC8357343 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution.

Minh Bui Quang BQ Dang Cuong Cao CC Vinh Le Sy LS Lanfear Robert R

Systematic biology 20210801 5

Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models; however, they are typically complicated and slow. In this article, we propose QMaker, a new ML method to estimate a general time-reversible $Q$ matrix from a large protein data set consisting of multiple sequence alignments. QMaker combines an efficient ML tree search algorithm, a model selection for handling the model heterog ...[more]

PMID: 33616668

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Project description:BackgroundMeasurement of muscle mass is important in the diagnosis of sarcopenia. Current measurement equipment are neither cost-effective nor standardized and cannot be used in a variety of medical settings. Some simple measurement tools have been proposed that are subjective and unvalidated. We aimed to develop and validate a new estimation equation in a more objective and standardized way, based on current proven variables that accurately reflect muscle mass.MethodsCross-sectional analysis with The National Health and Nutrition Examination Survey database for equation development and validation. Overall, 9875 participants were included for development (6913 participants) and validation (2962 participants), for whom the database included demographic data, physical measurements, and main biochemical indicators. Appendicular skeletal muscle mass (ASM) was estimated by dual-energy x-ray absorptiometry (DXA) and low muscle mass was defined by reference to five international diagnostic criteria. Linear regression was used to estimate the logarithm of the actual ASM from demographic data, physical measurements, and biochemical indicators.ResultsThis study of 9875 participants comprised 4492 females (49.0%), with a weighted mean (SE) age of 41.83 (0.36) years and range of 12 to 85 years. The estimated ASM equations performed well in the validation data set. The variability in estimated ASM was low compared with the actual ASM (R2 : Equation 1 = 0.91, Equation 4 = 0.89), with low bias (median difference: Equation 1 = -0.64, Equation 4 = 0.07; root mean square error: Equation 1 = 1.70 [1.69-1.70], Equation 4 = 1.85 [1.84-1.86]), high precision (interquartile range of the differences: Equation 1 = 1.87, Equation 4 = 2.17), and high efficacy in diagnosing low muscle mass (area under the curve: Equation 1 = 0.91 to 0.95, Equation 4 = 0.90 to 0.94).ConclusionsThe estimated ASM equations are accurate and simple and can be routinely applied clinically to estimate ASM and thus assess sarcopenia.

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QMaker: Fast and accurate method to estimate empirical models of protein evolution.

Publications

QMaker: Fast and Accurate Method to Estimate Empirical Models of Protein Evolution.

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