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Year 2023, Volume: 44 Issue: 1, 130 - 142, 26.03.2023
https://doi.org/10.17776/csj.1071349

Abstract

References

  • [1] Gambette P., Berry V., Paul C., The structure of level-k phylogenetic networks, Annual Symposium on Combinatorial Pattern Matching Springer, Berlin, Heidelberg, (2009, June). 289-300.
  • [2] Jansson J., Sung W. K., Inferring a level-1 phylogenetic network from a dense set of rooted triplets, Theoretical Computer Science, 363(1) (2006) 60-68.
  • [3] Van Iersel L., Keijsper J., Kelk S., Stougie L., Hagen F., Boekhout T., Constructing level-2 phylogenetic networks from triplets, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(4) (2009) 667-681.
  • [4] Gross E., Long C., Distinguishing phylogenetic networks. SIAM Journal on Applied Algebra and Geometry, 2(1) (2018) 72-93.
  • [5] Huber K. T., Moulton V., Semple C., Wu T., Quarnet inference rules for level-1 networks, Bulletin of Mathematical Biology, 80(8) (2018) 2137-2153.
  • [6] Huebler S., Morris R., Rusinko J., Tao Y. Constructing semi-directed level-1 phylogenetic networks from quarnets, (2019) arXiv preprint arXiv:1910.00048.
  • [7] Solís-Lemus C., Ané C., Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting, PLoS genetics, 12(3) (2016) e1005896.

The Structure of Level-2 Semi-directed Binary Phylogenetic Networks

Year 2023, Volume: 44 Issue: 1, 130 - 142, 26.03.2023
https://doi.org/10.17776/csj.1071349

Abstract

Phylogenetic trees describe evolution but due to hybridization events, recombination events or lateral gene transfer, it can be represented as a phylogenetic network. In phylogenetic networks, some of the branches of tree combine and create a reticulation node. Level of a network is decided to look at how many nodes in a connected component in a network. In this research, Int this paper, the structure of directed and undirected level-2 networks and how the can be decomposed into level-2 generators is studied..

References

  • [1] Gambette P., Berry V., Paul C., The structure of level-k phylogenetic networks, Annual Symposium on Combinatorial Pattern Matching Springer, Berlin, Heidelberg, (2009, June). 289-300.
  • [2] Jansson J., Sung W. K., Inferring a level-1 phylogenetic network from a dense set of rooted triplets, Theoretical Computer Science, 363(1) (2006) 60-68.
  • [3] Van Iersel L., Keijsper J., Kelk S., Stougie L., Hagen F., Boekhout T., Constructing level-2 phylogenetic networks from triplets, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(4) (2009) 667-681.
  • [4] Gross E., Long C., Distinguishing phylogenetic networks. SIAM Journal on Applied Algebra and Geometry, 2(1) (2018) 72-93.
  • [5] Huber K. T., Moulton V., Semple C., Wu T., Quarnet inference rules for level-1 networks, Bulletin of Mathematical Biology, 80(8) (2018) 2137-2153.
  • [6] Huebler S., Morris R., Rusinko J., Tao Y. Constructing semi-directed level-1 phylogenetic networks from quarnets, (2019) arXiv preprint arXiv:1910.00048.
  • [7] Solís-Lemus C., Ané C., Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting, PLoS genetics, 12(3) (2016) e1005896.
There are 7 citations in total.

Details

Primary Language English
Subjects Structural Biology, Mathematical Sciences, Statistics
Journal Section Natural Sciences
Authors

Nihan Özbaltan 0000-0003-0191-312X

Publication Date March 26, 2023
Submission Date February 10, 2022
Acceptance Date November 13, 2022
Published in Issue Year 2023Volume: 44 Issue: 1

Cite

APA Özbaltan, N. (2023). The Structure of Level-2 Semi-directed Binary Phylogenetic Networks. Cumhuriyet Science Journal, 44(1), 130-142. https://doi.org/10.17776/csj.1071349