title: A program for verification of phylogenetic network models.
abstract: Genetic material is transferred in a non-reproductive manner across species more frequently than commonly thought, particularly in the bacteria kingdom. On one hand, extant genomes are thus more properly considered as a fusion product of both reproductive and non-reproductive genetic transfers. This has motivated researchers to adopt phylogenetic networks to study genome evolution. On the other hand, a gene's evolution is usually tree-like and has been studied for over half a century. Accordingly, the relationships between phylogenetic trees and networks are the basis for the reconstruction and verification of phylogenetic networks. One important problem in verifying a network model is determining whether or not certain existing phylogenetic trees are displayed in a phylogenetic network. This problem is formally called the tree containment problem. It is NP-complete even for binary phylogenetic networks.
  
  
  
  We design an exponential time but efficient method for determining whether or not a phylogenetic tree is displayed in an arbitrary phylogenetic network. It is developed on the basis of the so-called reticulation-visible property of phylogenetic networks.
  
  
  
  A C-program is available for download on http://www.math.nus.edu.sg/∼matzlx/tcp_package
  
  
  
  matzlx@nus.edu.sg
  
  
  
  Supplementary data are available at Bioinformatics online.
authors: Department of Mathematics.
authors: Andreas D M
authors: AD
authors: Gunawan
authors: Department of Computer Science, National University of Singapore, Singapore 117417, Singapore.
authors: Bingxin
authors: B
authors: Lu
authors: Department of Mathematics.
authors: Louxin
authors: L
authors: Zhang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D016678:Genome; D008957:Models, Genetic; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D012984:Software