The Asymmetric Cluster Affinity Cost

Wagle, Sanket; Markin, Alexey; Górecki, Paweł; Anderson, Tavis K.; Eulenstein, Oliver

doi:10.1007/978-3-031-36911-7_9

Lecture Notes in Computer Science

2023

DOI: 10.1007/978-3-031-36911-7_9

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The Asymmetric Cluster Affinity Cost

Sanket Wagle

Alexey Markin

Paweł Górecki

et al.

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2024

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Asymmetric Cluster-Based Measures for Comparative Phylogenetics

Wagle,

Markin,

Górecki

et al. 2024

Journal of Computational Biology

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Phylogenetic inference and reconstruction methods generate hypotheses on evolutionary history. Competing inference methods are frequently used, and the evaluation of the generated hypotheses is achieved using tree comparison costs. The Robinson–Foulds (RF) distance is a widely used cost to compare the topology of two trees, but this cost is sensitive to tree error and can overestimate tree differences. To overcome this limitation, a refined version of the RF distance called the Cluster Affinity (CA) distance was introduced. However, CA distances are symmetric and cannot compare different types of trees. These asymmetric comparisons occur when gene trees are compared with species trees, when disparate datasets are integrated into a supertree, or when tree comparison measures are used to infer a phylogenetic network. In this study, we introduce a relaxation of the original Affinity distance to compare heterogeneous trees called the asymmetric CA cost. We also develop a biologically interpretable cost, the Cluster Support cost that normalizes by cluster size across gene trees. The characteristics of these costs are similar to the symmetric CA cost. We describe efficient algorithms, derive the exact diameters, and use these to standardize the cost to be applicable in practice. These costs provide objective, fine-scale, and biologically interpretable values that can assess differences and similarities between phylogenetic trees.

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Asymmetric Cluster-Based Measures for Comparative Phylogenetics

Wagle,

Markin,

Górecki

et al. 2024

Journal of Computational Biology

Self Cite

View full text Add to dashboard Cite

show abstract

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The Asymmetric Cluster Affinity Cost

Cited by 1 publication

References 26 publications

Asymmetric Cluster-Based Measures for Comparative Phylogenetics

Asymmetric Cluster-Based Measures for Comparative Phylogenetics

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