ArticleMolecular biology and evolution2014
Limited utility of residue masking for positive-selection inference.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models.Molecular biology and evolution · 2026Article
- Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.Molecular biology and evolution · 2024Review
- Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants.bioRxiv : the preprint server for biology · 2024Article
- Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses.Molecular biology and evolution · 2023Article
- Relative model selection of evolutionary substitution models can be sensitive to multiple sequence alignment uncertainty.BMC ecology and evolution · 2021Article
- Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences.BMC evolutionary biology · 2019Article
- Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation.Genome biology and evolution · 2017Article
- Intermediate divergence levels maximize the strength of structure-sequence correlations in enzymes and viral proteins.Protein science : a publication of the Protein Society · 2016Article
- Inferring Indel Parameters using a Simulation-based Approach.Genome biology and evolution · 2015Article
- Molecular Evolution of Drosophila Germline Stem Cell and Neural Stem Cell Regulating Genes.Genome biology and evolution · 2015Article
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3 authors.
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Abstract
Errors in multiple sequence alignments (MSAs) can reduce accuracy in positive-selection inference. Therefore, it has been suggested to filter MSAs before conducting further analyses. One widely used filter, Guidance, allows users to remove MSA positions aligned with low confidence. However, Guidance's utility in positive-selection inference has been disputed in the literature. We have conducted an extensive simulation-based study to characterize fully how Guidance impacts positive-selection inference, specifically for protein-coding sequences of realistic divergence levels. We also investigated whether novel scoring algorithms, which phylogenetically corrected confidence scores, and a new gap-penalization score-normalization scheme improved Guidance's performance. We found that no filter, including original Guidance, consistently benefitted positive-selection inferences. Moreover, all improvements detected were exceedingly minimal, and in certain circumstances, Guidance-based filters worsened inferences.
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Registered trials
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