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Constructing Minimal Phylogenetic Networks from Softwired Clusters is Fixed Parameter Tractable

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Abstract

Here we show that, given a set of clusters \({\mathcal{C}}\) on a set of taxa \({\mathcal{X}}\), where \(|{\mathcal{X}}|=n\), it is possible to determine in time f(k)⋅poly(n) whether there exists a level-≤k network (i.e. a network where each biconnected component has reticulation number at most k) that represents all the clusters in \({\mathcal{C}}\) in the softwired sense, and if so to construct such a network. This extends a result from Kelk et al. (in IEEE/ACM Trans. Comput. Biol. Bioinform. 9:517–534, 2012) which showed that the problem is polynomial-time solvable for fixed k. By defining “k-reticulation generators” analogous to “level-k generators”, we then extend this fixed parameter tractability result to the problem where k refers not to the level but to the reticulation number of the whole network.

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Algorithm 1
Algorithm 2
Algorithm 3
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Notes

  1. This is the definition when all reticulation vertices have indegree-2, for more general networks reticulation number is defined slightly differently. See the Preliminaries for more information.

  2. Alternatively, we say that a network N represents a cluster \(C \subset \mathcal{X}\) “in the hardwired sense” if there exists a tree edge (u,v) of N such that C is the set of leaf descendants of v.

  3. Otherwise \({\mathcal{C}}\) can be trivially represented by the star tree on \({\mathcal{X}}\).

  4. Note that to determine the reticulation number of a biconnected component, the indegree of each node is computed using only edges belonging to this biconnected component.

  5. Recall that, by Lemma 1 of [20], the existence of a level-k network representing a separating set of clusters \({\mathcal{C}}\) on \({\mathcal{X}}\) implies that a simple level-k network representing \({\mathcal{C}}\) has to exist.

  6. Note that the number of level-k generators grows rapidly in k, lying between 2k−1 and k!250k [8].

  7. Indeed, short sides can only be allocated taxa in two ways. Firstly, indirectly via Algorithm 1. Secondly, when there are no longer any unfinished long sides, at the very end of the entire procedure, in Algorithm 3.

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Authors and Affiliations

  1. Department of Knowledge Engineering (DKE), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands

    Steven Kelk

  2. ISEM, UMR 5554, CNRS, Univ. Montpellier 2, Place Eugène Bataillon, Montpellier, France

    Celine Scornavacca

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  1. Steven Kelk
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  2. Celine Scornavacca
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Correspondence to Celine Scornavacca.

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Kelk, S., Scornavacca, C. Constructing Minimal Phylogenetic Networks from Softwired Clusters is Fixed Parameter Tractable. Algorithmica 68, 886–915 (2014). https://doi.org/10.1007/s00453-012-9708-5

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