multistrap: boosting phylogenetic analyses with structural information Article Swipe
YOU?
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· 2025
· Open Access
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· DOI: https://doi.org/10.1038/s41467-024-55264-0
In a phylogeny, trustworthy reliability branch support estimates are as important as the tree itself. We show that reliability support values based on bootstrapping can be improved by combining sequence and structural information from proteins. Our approach relies on the systematic comparison of homologous intra-molecular structural distances. These variations exhibit less saturation than sequence-based Hamming distances and support the computation of tree-like distance matrices resolvable into phylogenetic trees using distance-based methods such as minimum evolution. These trees bear strong similarities to their sequence-based counterparts and allow the estimation of bootstrap support values, but they are sufficiently distinct so that their information content may be combined. The combined sequence and structure bootstrap support values yield improved discrimination between correct and incorrect branches. In this work we show that our approach, named multistrap, is suitable for the improvement of bootstrap branch support values using both predicted and experimental 3D structures.
Related Topics
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1038/s41467-024-55264-0
- https://www.nature.com/articles/s41467-024-55264-0.pdf
- OA Status
- gold
- Cited By
- 7
- References
- 50
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4406400545
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4406400545Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1038/s41467-024-55264-0Digital Object Identifier
- Title
-
multistrap: boosting phylogenetic analyses with structural informationWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-01-15Full publication date if available
- Authors
-
Athanasios Baltzis, Luisa Santus, Björn E. Langer, Cedrik Magis, Damien M. de Vienne, Olivier Gascuel, Leila Mansouri, Cédric NotredameList of authors in order
- Landing page
-
https://doi.org/10.1038/s41467-024-55264-0Publisher landing page
- PDF URL
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https://www.nature.com/articles/s41467-024-55264-0.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://www.nature.com/articles/s41467-024-55264-0.pdfDirect OA link when available
- Concepts
-
Boosting (machine learning), Phylogenetic tree, Phylogenetics, Computer science, Computational biology, Evolutionary biology, Biology, Artificial intelligence, Genetics, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
7Total citation count in OpenAlex
- Citations by year (recent)
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2025: 7Per-year citation counts (last 5 years)
- References (count)
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50Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.computation | 59 |
| abstract_inverted_index.improvement | 135 |
| abstract_inverted_index.information | 32, 100 |
| abstract_inverted_index.multistrap, | 130 |
| abstract_inverted_index.reliability | 4, 18 |
| abstract_inverted_index.structures. | 147 |
| abstract_inverted_index.trustworthy | 3 |
| abstract_inverted_index.counterparts | 83 |
| abstract_inverted_index.experimental | 145 |
| abstract_inverted_index.phylogenetic | 66 |
| abstract_inverted_index.similarities | 79 |
| abstract_inverted_index.sufficiently | 95 |
| abstract_inverted_index.bootstrapping | 23 |
| abstract_inverted_index.discrimination | 115 |
| abstract_inverted_index.distance-based | 69 |
| abstract_inverted_index.sequence-based | 53, 82 |
| abstract_inverted_index.intra-molecular | 44 |
| cited_by_percentile_year.max | 99 |
| cited_by_percentile_year.min | 98 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 8 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/16 |
| sustainable_development_goals[0].score | 0.5199999809265137 |
| sustainable_development_goals[0].display_name | Peace, Justice and strong institutions |
| sustainable_development_goals[1].id | https://metadata.un.org/sdg/10 |
| sustainable_development_goals[1].score | 0.46000000834465027 |
| sustainable_development_goals[1].display_name | Reduced inequalities |
| citation_normalized_percentile.value | 0.98311696 |
| citation_normalized_percentile.is_in_top_1_percent | True |
| citation_normalized_percentile.is_in_top_10_percent | True |