Computing a Consensus of Multilabeled Trees

@inproceedings{Huber2012ComputingAC,
  title={Computing a Consensus of Multilabeled Trees},
  author={Katharina T. Huber and Vincent Moulton and Andreas Spillner and Sabine Storandt and Radosław Suchecki},
  booktitle={ALENEX},
  year={2012}
}
In this paper we consider two challenging problems that arise in the context of computing a consensus of a collection of multilabeled trees, namely (1) selecting a compatible collection of clusters on a multiset from an ordered list of such clusters and (2) optimally refining high degree vertices in a multilabeled tree. Forming such a consensus is part of an approach to reconstruct the evolutionary history of a set of species for which events such as genome duplication and hybridization have… 

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References

SHOWING 1-10 OF 13 REFERENCES

Computing a Smallest Multilabeled Phylogenetic Tree from Rooted Triplets

TLDR
It is proved that even the very restricted case of determining if there exists a MUL tree consistent with the input and having just one leaf duplication is an NP-hard problem, and the general minimization problem is difficult to approximate.

The Complexity of Deriving Multi-Labeled Trees from Bipartitions

TLDR
It is shown that it is NP-hard to decide whether a collection of bipartitions of a multiset can be represented by a multi-labeled tree, and a fixed-parameter algorithm is obtained in terms of a parameter associated to the given multisets.

Inferring polyploid phylogenies from multiply-labeled gene trees

TLDR
A heuristic method for computing a consensus tree of multiply-labeled trees and illustrates the applicability of the method using two collections of trees for plants of the genus Silene, that involve several allopolyploids at different levels.

From Gene Trees to Species Trees through a Supertree Approach

TLDR
This work proposes a novel approach to tackle the problem of inferring a species tree from a set of multi-labeled gene trees, mainly to transform a collection of MUL trees into aCollection of evolutionary trees, each containing single copies of labels.

Phylogenetic networks from multi-labelled trees

TLDR
Based on the knowledge of a multi-labelled tree relating collection of polyploids, this work presents a canonical construction of a phylogenetic network that exhibits the tree and proves that the resulting network is in some well-defined sense a minimal network having this property.

The probabilities of rooted tree-shapes generated by random bifurcation

  • E. Harding
  • Mathematics, Computer Science
    Advances in Applied Probability
  • 1971
TLDR
The account of enumeration collates much previous work and attempts a complete perspective of the problems and their solutions of attempting to reconstruct evolutionary trees by the statistical approach of Cavalli-Sforza and Edwards.

Allopolyploidization and evolution of species with reduced floral structures in Lepidium L. (Brassicaceae)

TLDR
Phylogenetic analysis of the PI intron suggests that many species in the New World have originated from allopolyploidization, and that this is correlated with floral reduction, and interspecific hybrids were generated to understand why allopolyPloidization is associated with reduced flowers.

Origin and Evolution of a Circumpolar Polyploid Species Complex in Silene (Caryophyllaceae) Inferred from Low Copy Nuclear RNA Polymerase Introns, rDNA, and Chloroplast DNA

TLDR
Phylogenetic analyses of two chloroplast and five putatively unlinked nuclear DNA regions were used to explore the evolutionary relationships of a circumpolar arctic polyploid species complex in Silene, showing small deviations from the general pattern explained by alloploidy.