On Reduced Amino Acid Alphabets for Phylogenetic Inference

Susko, E.; Roger, A. J.

doi:10.1093/molbev/msm144

Cited by 179Genomics and Phylogenetic StudiesRNA and protein synthesis mechanismsFractal and DNA sequence analysis

On Reduced Amino Acid Alphabets for Phylogenetic Inference

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Susko, E., Roger, A. J.·2007·Molecular Biology and Evolution

DOI 10.1093/molbev/msm144

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Abstract

We investigate the use of Markov models of evolution for reduced amino acid alphabets or bins of amino acids. The use of reduced amino acid alphabets can ameliorate effects of model misspecification and saturation. We present algorithms for 2 different ways of automating the construction of bins: minimizing criteria based on properties of rate matrices and minimizing criteria based on properties of alignments. By simulation, we show that in the absence of model misspecification, the loss of information due to binning is found to be insubstantial, and the use of Markov models at the binned level is found to be almost as effective as the more appropriate missing data approach. By applying these approaches to real data sets where compositional heterogeneity and/or saturation appear to be causing biased tree estimation, we find that binning can improve topological estimation in practice.

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Matrix recoding has been proposed as a solution for both compositional heterogeneity and substitution saturation.
“Based on this foundation, matrix recoding has been proposed as a solution for both compositional heterogeneity and substitution saturation (Blanquart and Lartillot 2006; Susko and Roger 2007).”
From Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses (2019) · cites this paper as Susko and Roger 2007
The number of possible amino acid binning schemes for a given number of states is very large, making an exhaustive search computationally intractable.
“the number of possible bins is very large”
From Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses (2019) · cites this paper as Susko and Roger (2007)
In all cases, the intra-bin substitution scores generated by the authors' best binning strategies were higher than those proposed by Susko and Roger (2007), except for one which had an equal score.
“in all cases, the scores we generated were higher, except for one which had an equal score”
From Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses (2019) · cites this paper as Susko and Roger (2007)
Data-recoding methods reduce compositional heterogeneity in the WhelanD20 and Chang datasets.
“We show that data-recoding methods [13-15] reduce compositional heterogeneity in these datasets”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [14]
Amino acid recoding has long been considered a powerful strategy to reduce compositional heterogeneity and saturation in the data.
“Amino acid recoding has long been considered as a powerful strategy to reduce compositional heterogeneity and saturation in the data [7, 13-15, 31-36]”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [14]

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A New Information Theoretic Approach Shows that Mixture Models Outperform Partition Models for Phylogenetic Analyses of Amino Acid DataPreprint
Ren, H., Jiang, C., Wong, T. K. F., Shao, Y., Susko, E., Minh, B. Q., & Lanfear, R. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.16.712229
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Authors: Susko, E., & Roger, A. J.
Affiliations: Dalhousie University (CA)
Corresponding author: Susko, E.
ORCID: Susko, E.
Roger, A. J.
Venue: Molecular Biology and Evolution
Publisher: Oxford University Press (OUP)
Published: 2007-05-23
Volume: 24
Issue: 9
Pages: 2139-2150
ISSN: 0737-4038 (ISSN-L)
1537-1719
DOI: 10.1093/molbev/msm144
OpenAlex: W2020680099
Cited by: 177
References: 41
Citations by year: 2026: 8 · 2025: 9 · 2024: 10 · 2023: 12 · 2022: 16 · 2021: 19 · 2020: 16 · 2019: 23 · 2018: 15 · 2017: 6 · 2016: 6 · 2015: 2 · 2014: 4 · 2013: 2 · 2012: 4
FWCI: 2.39
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Molecular Biology and Evolution (publishedVersion)
PubMed (publishedVersion)
Funders: Canadian Institute for Advanced Research
Canadian Institutes of Health Research
Natural Sciences and Engineering Research Council of Canada
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fractal and DNA sequence analysis
Keywords: reduced amino acid alphabet, phylogenetic inference, model misspecification, saturation, rate matrix, compositional heterogeneity, missing data
MeSH terms: Algorithms, Amino Acid Sequence, Amino Acids, Animals, Chloroplasts, Computer Simulation, Markov Chains, Molecular Sequence Data, Nuclear Proteins, Phylogeny, Plant Proteins, Plants, Sequence Analysis, Protein, Mitochondrial Proteins

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On Reduced Amino Acid Alphabets for Phylogenetic Inference

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