NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Reconstructing reticulate evolution in species: theory and practice
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Seeing the trees and their branches in the network is hard
Theoretical Computer Science
All-pairs ancestor problems inweighted dags
ESCAPE'07 Proceedings of the First international conference on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies
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Phylogenetic networks model evolutionary histories in the presence of non-treelike events such as hybrid speciation and horizontal gene transfer. In spite of their widely acknowledged importance, very little is known about phylogenetic networks, which have so far been studied mostly for specific datasets. Even when the evolutionary history of a set of species is non-treelike, individual genes in these species usually evolve in a treelike fashion. An important question, then, is whether a gene tree is “contained” inside a species network. This information is used to detect the presence of events such as horizontal gene transfer and hybrid speciation. Another question of interest for biologists is whether a group of taxa forms a clade based on a given phylogeny. This can be efficiently answered when the phylogeny is a tree simply by inspecting the edges of the tree, whereas no efficient solution currently exists for the problem when the phylogeny is a network. In this paper, we give polynomial-time algorithms for answering the above two questions.