NANUQ+: A divide-and-conquer approach to network estimation
Abstract Inference of a species network from genomic data remains a difficult problem, with recent progress mostly limited to the level-1 case. However, inference of the Tree of Blobs of a network, showing only the network’s cut edges, can be performed for any network by TINNiK, suggesting a divide-...
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| Format: | Article |
| Language: | English |
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BMC
2025-07-01
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| Series: | Algorithms for Molecular Biology |
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| Online Access: | https://doi.org/10.1186/s13015-025-00274-w |
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| author | Elizabeth S. Allman Hector Baños John A. Rhodes Kristina Wicke |
| author_facet | Elizabeth S. Allman Hector Baños John A. Rhodes Kristina Wicke |
| author_sort | Elizabeth S. Allman |
| collection | DOAJ |
| description | Abstract Inference of a species network from genomic data remains a difficult problem, with recent progress mostly limited to the level-1 case. However, inference of the Tree of Blobs of a network, showing only the network’s cut edges, can be performed for any network by TINNiK, suggesting a divide-and-conquer approach to network inference where the tree’s multifurcations are individually resolved to give more detailed structure. Here we develop a method, $$\text {NANUQ}^+$$ NANUQ + , to quickly perform such a level-1 resolution. Viewed as part of the NANUQ pipeline for fast level-1 inference, this gives tools for both understanding when the level-1 assumption is likely to be met and for exploring all highly-supported resolutions to cycles. |
| format | Article |
| id | doaj-art-809c678d226c4170b4e887d9da10eb4b |
| institution | Kabale University |
| issn | 1748-7188 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Algorithms for Molecular Biology |
| spelling | doaj-art-809c678d226c4170b4e887d9da10eb4b2025-08-20T03:42:44ZengBMCAlgorithms for Molecular Biology1748-71882025-07-0120112510.1186/s13015-025-00274-wNANUQ+: A divide-and-conquer approach to network estimationElizabeth S. Allman0Hector Baños1John A. Rhodes2Kristina Wicke3Department of Mathematics and Statistics, University of Alaska FairbanksDepartment of Mathematics, California State University San BernardinoDepartment of Mathematics and Statistics, University of Alaska FairbanksDepartment of Mathematical Sciences, New Jersey Institute of TechnologyAbstract Inference of a species network from genomic data remains a difficult problem, with recent progress mostly limited to the level-1 case. However, inference of the Tree of Blobs of a network, showing only the network’s cut edges, can be performed for any network by TINNiK, suggesting a divide-and-conquer approach to network inference where the tree’s multifurcations are individually resolved to give more detailed structure. Here we develop a method, $$\text {NANUQ}^+$$ NANUQ + , to quickly perform such a level-1 resolution. Viewed as part of the NANUQ pipeline for fast level-1 inference, this gives tools for both understanding when the level-1 assumption is likely to be met and for exploring all highly-supported resolutions to cycles.https://doi.org/10.1186/s13015-025-00274-wPhylogenetic networkLevel-1Tree of blobsMultispecies coalescent |
| spellingShingle | Elizabeth S. Allman Hector Baños John A. Rhodes Kristina Wicke NANUQ+: A divide-and-conquer approach to network estimation Algorithms for Molecular Biology Phylogenetic network Level-1 Tree of blobs Multispecies coalescent |
| title | NANUQ+: A divide-and-conquer approach to network estimation |
| title_full | NANUQ+: A divide-and-conquer approach to network estimation |
| title_fullStr | NANUQ+: A divide-and-conquer approach to network estimation |
| title_full_unstemmed | NANUQ+: A divide-and-conquer approach to network estimation |
| title_short | NANUQ+: A divide-and-conquer approach to network estimation |
| title_sort | nanuq a divide and conquer approach to network estimation |
| topic | Phylogenetic network Level-1 Tree of blobs Multispecies coalescent |
| url | https://doi.org/10.1186/s13015-025-00274-w |
| work_keys_str_mv | AT elizabethsallman nanuqadivideandconquerapproachtonetworkestimation AT hectorbanos nanuqadivideandconquerapproachtonetworkestimation AT johnarhodes nanuqadivideandconquerapproachtonetworkestimation AT kristinawicke nanuqadivideandconquerapproachtonetworkestimation |