multistrap: boosting phylogenetic analyses with structural information

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  • dc.contributor.author Baltzis, Athanasios
  • dc.contributor.author Santus, Luisa
  • dc.contributor.author Langer, Björn E.
  • dc.contributor.author Magis, Cedrik
  • dc.contributor.author de Vienne, Damien M.
  • dc.contributor.author Gascuel, Olivier
  • dc.contributor.author Mansouri, Leila
  • dc.contributor.author Notredame, Cedric
  • dc.date.accessioned 2025-02-25T07:33:22Z
  • dc.date.available 2025-02-25T07:33:22Z
  • dc.date.issued 2025
  • dc.description.abstract 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.
  • dc.description.sponsorship The research leading to these results has received funding from the Spanish Ministry of Science and Innovation (PRE2018-085039 funds for predoctoral contract funded by MICIU/AEI/10.13039/501100011033 and by the FSE invest in your future (L.M.), PRE2021-097947 funds for predoctoral contract funded by MICIU/AEI/10.13039/501100011033 and by FSE+ (L.S.)). We acknowledge support of the Spanish Ministry of Science and Innovation through the Centro de Excelencia Severo Ochoa (CEX2020-001049-S, MCIN/AEI /10.13039/501100011033), and the Generalitat de Catalunya through the CERCA programme (C.N.). O.G. is supported by the Paris Artificial Intelligence Research Institute (PRAIRIE, ANR-19-P3IA-0001). We are grateful to the CRG Core Technologies Programme for their support and assistance in this work. The authors are also very grateful to Edward L. Braun who extensively reviewed the manuscript and proposed very useful edits and suggestions, especially with respect to the saturation analysis.
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Baltzis A, Santus L, Langer BE, Magis C, de Vienne DM, Gascuel O, et al. multistrap: boosting phylogenetic analyses with structural information. Nat Commun. 2025 Jan 15;16(1):293. DOI: 10.1038/s41467-024-55264-0
  • dc.identifier.doi http://dx.doi.org/10.1038/s41467-024-55264-0
  • dc.identifier.issn 2041-1723
  • dc.identifier.uri http://hdl.handle.net/10230/69729
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nat Commun. 2025 Jan 15;16(1):293
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PRE2018-085039
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PRE2021-097947
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/CEX2020-001049-S
  • dc.rights © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/
  • dc.subject.keyword Phylogenetics
  • dc.subject.keyword Phylogeny
  • dc.subject.keyword Structural biology
  • dc.title multistrap: boosting phylogenetic analyses with structural information
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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