title: Tanglegrams for rooted phylogenetic trees and networks.
abstract: BACKGROUND
  In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multi-gene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks.
  
  
  RESULTS
  In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets.
  
  
  BACKGROUND
  The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org.
  
  
  BACKGROUND
  scornava@informatik.uni-tuebingen.de; huson@informatik.uni-tuebingen.de.
authors.affiliation: Center for Bioinformatics (ZBIT), Tübingen University, Sand 14, 72076 Tübingen, Germany. scornava@informatik.uni-tuebingen.de
authors.forename: Celine
authors.initials: C
authors.lastname: Scornavacca
authors.forename: Franziska
authors.initials: F
authors.lastname: Zickmann
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Huson
mesh_terms: D000465:Algorithms; D000818:Animals; D005075:Biological Evolution; D001695:Biology / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030681:Ficus / Q000235:genetics; D022761:Gene Transfer, Horizontal; D006824:Hybridization, Genetic; D010802:Phylogeny; D014863:Wasps / Q000235:genetics