title: A novel algorithm and web-based tool for comparing two alternative phylogenetic trees.
abstract: CONCLUSIONS
  We describe an algorithm and software tool for comparing alternative phylogenetic trees. The main application of the software is to compare phylogenies obtained using different phylogenetic methods for some fixed set of species or obtained using different gene sequences from those species. The algorithm pairs up each branch in one phylogeny with a matching branch in the second phylogeny and finds the optimum 1-to-1 map between branches in the two trees in terms of a topological score. The software enables the user to explore the corresponding mapping between the phylogenies interactively, and clearly highlights those parts of the trees that differ, both in terms of topology and branch length.
  
  
  BACKGROUND
  The software is implemented as a Java applet at http://www.mrc-bsu.cam.ac.uk/personal/thomas/phylo_comparison/comparison_page.html. It is also available on request from the authors.
authors.affiliation: Biostatistics Unit, Medical Research Council, Cambridge, UK. thomas.nye@mrc-bsu.cam.ac.uk
authors.forename: Tom M W
authors.initials: TM
authors.lastname: Nye
authors.forename: Pietro
authors.initials: P
authors.lastname: Liò
authors.forename: Walter R
authors.initials: WR
authors.lastname: Gilks
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D006678:HIV / Q000235:genetics; D020407:Internet; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D011381:Programming Languages; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface