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Evaluation of the RelatiPerformance of the Subflattenings Method for Phylogenetic Inference
Citation
Stevenson, J and Holland, B and Charleston, M and Sumner, J, Evaluation of the RelatiPerformance of the Subflattenings Method for Phylogenetic Inference, Bulletin of Mathematical Biology, 85, (19) pp. 1-23. ISSN 1522-9602 (2023) [Refereed Article]
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DOI: doi:10.1007/s11538-023-01120-z
Abstract
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny—and by extension the complete tree—using pattern counts from a sequence alignment. The relatively small number of possible internal edges among a set of taxa (compared to the number of binary trees) makes these methods attractive; however, more could be done to evaluate their effectiveness for inferring phylogenetic trees. This is the case particularly for subflattenings, and the work we present here makes progress in this area. We introduce software for constructing and evaluating subflattenings for splits, utilising a number of methods to make computing subflattenings more tractable. We then present the results of simulations we have performed in order to compare the effectiveness of subflattenings to that of flattenings in terms of split score distributions, and susceptibility to possible biases. We find that subflattenings perform similarly to flattenings in terms of the distribution of split scores on the trees we examined, but may be less affected by bias arising from both split size/balance and long branch attraction. These insights are useful for developing effective algorithms to utilise these tools for the purpose of inferring phylogenetic trees.
Item Details
| Item Type: | Refereed Article |
|---|---|
| Keywords: | Phylogenetics · Flattening · Subflattening · Splits · Rank |
| Research Division: | Mathematical Sciences |
| Research Group: | Applied mathematics |
| Research Field: | Biological mathematics |
| Objective Division: | Expanding Knowledge |
| Objective Group: | Expanding knowledge |
| Objective Field: | Expanding knowledge in the mathematical sciences |
| UTAS Author: | Stevenson, J (Mr Joshua Stevenson) |
| UTAS Author: | Holland, B (Professor Barbara Holland) |
| UTAS Author: | Charleston, M (Professor Michael Charleston) |
| UTAS Author: | Sumner, J (Associate Professor Jeremy Sumner) |
| ID Code: | 155194 |
| Year Published: | 2023 |
| Deposited By: | Mathematics |
| Deposited On: | 2023-02-02 |
| Last Modified: | 2023-02-02 |
| Downloads: | 0 |
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