Literature DB >> 18177903

Tripartitions do not always discriminate phylogenetic networks.

Gabriel Cardona1, Francesc Rosselló, Gabriel Valiente.   

Abstract

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the study of reconstructibility of phylogenetic networks, Moret, Nakhleh, Warnow and collaborators introduced the so-called tripartition metric for phylogenetic networks. In this paper we show that, in fact, this tripartition metric does not satisfy the separation axiom of distances (zero distance means isomorphism, or, in a more relaxed version, zero distance means indistinguishability in some specific sense) in any of the subclasses of phylogenetic networks where it is claimed to do so. We also present a subclass of phylogenetic networks whose members can be singled out by means of their sets of tripartitions (or even clusters), and hence where the latter can be used to define a meaningful metric.

Mesh:

Year:  2007        PMID: 18177903     DOI: 10.1016/j.mbs.2007.11.003

Source DB:  PubMed          Journal:  Math Biosci        ISSN: 0025-5564            Impact factor:   2.144


  10 in total

1.  A distance metric for a class of tree-sibling phylogenetic networks.

Authors:  Gabriel Cardona; Mercè Llabrés; Francesc Rosselló; Gabriel Valiente
Journal:  Bioinformatics       Date:  2008-05-12       Impact factor: 6.937

2.  Characterization of phylogenetic networks with NetTest.

Authors:  Miguel Arenas; Mateus Patricio; David Posada; Gabriel Valiente
Journal:  BMC Bioinformatics       Date:  2010-05-20       Impact factor: 3.169

3.  The comparison of tree-sibling time consistent phylogenetic networks is graph isomorphism-complete.

Authors:  Gabriel Cardona; Mercè Llabrés; Francesc Rosselló; Gabriel Valiente
Journal:  ScientificWorldJournal       Date:  2014-04-02

4.  Reconstructible phylogenetic networks: do not distinguish the indistinguishable.

Authors:  Fabio Pardi; Celine Scornavacca
Journal:  PLoS Comput Biol       Date:  2015-04-07       Impact factor: 4.475

5.  A Metric on the Space of Partly Reduced Phylogenetic Networks.

Authors:  Juan Wang
Journal:  Biomed Res Int       Date:  2016-06-23       Impact factor: 3.411

6.  A Metric on the Space of kth-order reduced Phylogenetic Networks.

Authors:  Juan Wang; Maozu Guo
Journal:  Sci Rep       Date:  2017-06-09       Impact factor: 4.379

7.  The Generalized Robinson-Foulds Distance for Phylogenetic Trees.

Authors:  Mercè Llabrés; Francesc Rosselló; Gabriel Valiente
Journal:  J Comput Biol       Date:  2021-10-29       Impact factor: 1.479

8.  Characterization of reticulate networks based on the coalescent with recombination.

Authors:  Miguel Arenas; Gabriel Valiente; David Posada
Journal:  Mol Biol Evol       Date:  2008-10-15       Impact factor: 16.240

9.  Using supernetworks to distinguish hybridization from lineage-sorting.

Authors:  Barbara R Holland; Steffi Benthin; Peter J Lockhart; Vincent Moulton; Katharina T Huber
Journal:  BMC Evol Biol       Date:  2008-07-14       Impact factor: 3.260

10.  A perl package and an alignment tool for phylogenetic networks.

Authors:  Gabriel Cardona; Francesc Rosselló; Gabriel Valiente
Journal:  BMC Bioinformatics       Date:  2008-03-27       Impact factor: 3.169

  10 in total

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