ArticleEntropy (Basel, Switzerland)2019
Phylogenetic weighting does little to improve the accuracy of evolutionary coupling analyses.
Article in Entropy (Basel, Switzerland), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed.
- Inference and Visualization of Complex Genotype-Phenotype Maps.Molecular biology and evolution · 2026Article
- Inference and visualization of complex genotype-phenotype maps withbioRxiv : the preprint server for biology · 2025Article
- Reconstruction of Ancestral Protein Sequences Using Autoregressive Generative Models.Molecular biology and evolution · 2025Article
- Impact of phylogeny on the inference of functional sectors from protein sequence data.PLoS computational biology · 2024Article
- Impact of phylogeny on structural contact inference from protein sequence data.Journal of the Royal Society, Interface · 2023Article
- Protein language models trained on multiple sequence alignments learn phylogenetic relationships.Nature communications · 2022Article
- Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences.PLoS computational biology · 2022Article
- Extracting phylogenetic dimensions of coevolution reveals hidden functional signals.Scientific reports · 2022Article
- On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins.PLoS computational biology · 2021Article
- Information Theory in Molecular Evolution: From Models to Structures and Dynamics.Entropy (Basel, Switzerland) · 2021Article
- Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting.Entropy (Basel, Switzerland) · 2020Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
Homologous sequence alignments contain important information about the constraints that shape protein family evolution. Correlated changes between different residues, for instance, can be highly predictive of physical contacts within three-dimensional structures. Detecting such co-evolutionary signals via direct coupling analysis is particularly challenging given the shared phylogenetic history and uneven sampling of different lineages from which protein sequences are derived. Current best practices for mitigating such effects include sequence-identity-based weighting of input sequences and
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