title: Taxon ordering in phylogenetic trees by means of evolutionary algorithms.
abstract: BACKGROUND
  In in a typical "left-to-right" phylogenetic tree, the vertical order of taxa is meaningless, as only the branch path between them reflects their degree of similarity. To make unresolved trees more informative, here we propose an innovative Evolutionary Algorithm (EA) method to search the best graphical representation of unresolved trees, in order to give a biological meaning to the vertical order of taxa.
  
  
  METHODS
  Starting from a West Nile virus phylogenetic tree, in a (1 + 1)-EA we evolved it by randomly rotating the internal nodes and selecting the tree with better fitness every generation. The fitness is a sum of genetic distances between the considered taxon and the r (radius) next taxa. After having set the radius to the best performance, we evolved the trees with (λ + μ)-EAs to study the influence of population on the algorithm.
  
  
  RESULTS
  The (1 + 1)-EA consistently outperformed a random search, and better results were obtained setting the radius to 8. The (λ + μ)-EAs performed as well as the (1 + 1), except the larger population (1000 + 1000).
  
  
  CONCLUSIONS
  The trees after the evolution showed an improvement both of the fitness (based on a genetic distance matrix, then close taxa are actually genetically close), and of the biological interpretation. Samples collected in the same state or year moved close each other, making the tree easier to interpret. Biological relationships between samples are also easier to observe.
authors: Department of Animal Production, Epidemiology and Ecology, Faculty of Veterinary Medicine, University of Torino, Via Leonardo da Vinci 44, 10095, Grugliasco (TO), Italy. mario.giacobini@unito.it.
authors: Francesco
authors: F
authors: Cerutti
authors: Luigi
authors: L
authors: Bertolotti
authors: Tony L
authors: TL
authors: Goldberg
authors: Mario
authors: M
authors: Giacobini