multistrap: boosting phylogenetic analyses with structural information
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 comparis...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-55264-0 |
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| author | Athanasios Baltzis Luisa Santus Björn E. Langer Cedrik Magis Damien M. de Vienne Olivier Gascuel Leila Mansouri Cedric Notredame |
| author_facet | Athanasios Baltzis Luisa Santus Björn E. Langer Cedrik Magis Damien M. de Vienne Olivier Gascuel Leila Mansouri Cedric Notredame |
| author_sort | Athanasios Baltzis |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-f2660669e5b4447e99fa9e09ea803405 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-f2660669e5b4447e99fa9e09ea8034052025-01-19T12:30:47ZengNature PortfolioNature Communications2041-17232025-01-0116111410.1038/s41467-024-55264-0multistrap: boosting phylogenetic analyses with structural informationAthanasios Baltzis0Luisa Santus1Björn E. Langer2Cedrik Magis3Damien M. de Vienne4Olivier Gascuel5Leila Mansouri6Cedric Notredame7Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyUniv Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558Institut de Systématique, Evolution, Biodiversité (UMR 7205—CNRS, Muséum National d’Histoire Naturelle, SU, EPHE UA)Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and TechnologyAbstract 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.https://doi.org/10.1038/s41467-024-55264-0 |
| spellingShingle | Athanasios Baltzis Luisa Santus Björn E. Langer Cedrik Magis Damien M. de Vienne Olivier Gascuel Leila Mansouri Cedric Notredame multistrap: boosting phylogenetic analyses with structural information Nature Communications |
| title | multistrap: boosting phylogenetic analyses with structural information |
| title_full | multistrap: boosting phylogenetic analyses with structural information |
| title_fullStr | multistrap: boosting phylogenetic analyses with structural information |
| title_full_unstemmed | multistrap: boosting phylogenetic analyses with structural information |
| title_short | multistrap: boosting phylogenetic analyses with structural information |
| title_sort | multistrap boosting phylogenetic analyses with structural information |
| url | https://doi.org/10.1038/s41467-024-55264-0 |
| work_keys_str_mv | AT athanasiosbaltzis multistrapboostingphylogeneticanalyseswithstructuralinformation AT luisasantus multistrapboostingphylogeneticanalyseswithstructuralinformation AT bjornelanger multistrapboostingphylogeneticanalyseswithstructuralinformation AT cedrikmagis multistrapboostingphylogeneticanalyseswithstructuralinformation AT damienmdevienne multistrapboostingphylogeneticanalyseswithstructuralinformation AT oliviergascuel multistrapboostingphylogeneticanalyseswithstructuralinformation AT leilamansouri multistrapboostingphylogeneticanalyseswithstructuralinformation AT cedricnotredame multistrapboostingphylogeneticanalyseswithstructuralinformation |