title: Comparison of phylogenetic trees through alignment of embedded evolutionary distances.
abstract: BACKGROUND
  The understanding of evolutionary relationships is a fundamental aspect of modern biology, with the phylogenetic tree being a primary tool for describing these associations. However, comparison of trees for the purpose of assessing similarity and the quantification of various biological processes remains a significant challenge.
  
  
  RESULTS
  We describe a novel approach for the comparison of phylogenetic distance information based on the alignment of representative high-dimensional embeddings (xCEED: Comparison of Embedded Evolutionary Distances). The xCEED methodology, which utilizes multidimensional scaling and Procrustes-related superimposition approaches, provides the ability to measure the global similarity between trees as well as incongruities between them. We demonstrate the application of this approach to the prediction of coevolving protein interactions and demonstrate its improved performance over the mirrortree, tol-mirrortree, phylogenetic vector projection, and partial correlation approaches. Furthermore, we show its applicability to both the detection of horizontal gene transfer events as well as its potential use in the prediction of interaction specificity between a pair of multigene families.
  
  
  CONCLUSIONS
  These approaches provide additional tools for the study of phylogenetic trees and associated evolutionary processes. Source code is available at http://gomezlab.bme.unc.edu/tools.
authors.affiliation: Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. kbchoi@cs.unc.edu
authors.forename: Kwangbom
authors.initials: K
authors.lastname: Choi
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Gomez
mesh_terms: D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*