Encoding and constructing 1-nested phylogenetic networks with trinets
From MaRDI portal
Abstract: Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from biological data using {em triplets}, i.e. binary phylogenetic trees on 3-element subsets of a given set of species. However, a fundamental problem with this approach is that the triplets displayed by a phylogenetic network do not necessary uniquely determine or {em encode} the network. Here we propose an alternative approach to encoding and constructing phylogenetic networks, which uses phylogenetic networks on 3-element subsets of a set, or {em trinets}, rather than triplets. More specifically, we show that for a special, well-studied type of phylogenetic network called a 1-nested network, the trinets displayed by a 1-nested network always encode the network. We also present an efficient algorithm for deciding whether a {em dense} set of trinets (i.e. one that contains a trinet on every 3-element subset of a set) can be displayed by a 1-nested network or not and, if so, constructs that network. In addition, we discuss some potential new directions that this new approach opens up for constructing and comparing phylogenetic networks.
Recommendations
- Trinets encode tree-child and level-2 phylogenetic networks
- On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters
- Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets
- Trinets encode orchard phylogenetic networks
- Constructing the simplest possible phylogenetic network from triplets
Cites work
- scientific article; zbMATH DE number 1088267 (Why is no real title available?)
- scientific article; zbMATH DE number 1945190 (Why is no real title available?)
- scientific article; zbMATH DE number 1865935 (Why is no real title available?)
- A fast algorithm for finding dominators in a flowgraph
- A supertree method for rooted trees
- Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network
- Computing the maximum agreement of phylogenetic networks
- Constructing the maximum consensus tree from rooted Triples
- Constructing the simplest possible phylogenetic network from triplets
- Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions
- Inferring a level-1 phylogenetic network from a dense set of rooted triplets
- Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time
- New results on optimizing rooted triplets consistency
- On encodings of phylogenetic networks of bounded level
- On the complexity of constructing evolutionary trees
- Tripartitions do not always discriminate phylogenetic networks
Cited in
(25)- Phylogenetic networks that are their own fold-ups
- Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes
- Trinets encode orchard phylogenetic networks
- Trinets encode tree-child and level-2 phylogenetic networks
- Beyond representing orthology relations by trees
- Quarnet inference rules for level-1 networks
- Reconstructing tree-child networks from reticulate-edge-deleted subnetworks
- Leaf-reconstructibility of phylogenetic networks
- Autopolyploidy, allopolyploidy, and phylogenetic networks with horizontal arcs
- On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters
- Classes of explicit phylogenetic networks and their biological and mathematical significance
- On encodings of phylogenetic networks of bounded level
- Constructing the Simplest Possible Phylogenetic Network from Triplets
- Computing consensus networks for collections of 1-nested phylogenetic networks
- The weighted total cophenetic index: a novel balance index for phylogenetic networks
- An algorithm for reconstructing level-2 phylogenetic networks from trinets
- Uprooted phylogenetic networks
- Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks
- From modular decomposition trees to level-1 networks: pseudo-cographs, polar-cats and prime polar-cats
- The hybrid number of a ploidy profile
- Reconstruction of LGT networks from tri-LGT-nets
- A cubic-time algorithm for computing the trinet distance between level-1 networks
- Caterpillars on three and four leaves are sufficient to binary normal networks
- Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets
- Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations
This page was built for publication: Encoding and constructing 1-nested phylogenetic networks with trinets
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2375949)
