title: Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.
abstract: BACKGROUND
  Available methods to simulate nucleotide or amino acid data typically use Markov models to simulate each position independently. These approaches are not appropriate to assess the performance of combinatorial and probabilistic methods that look for coevolving positions in nucleotide or amino acid sequences.
  
  
  RESULTS
  We have developed a web-based platform that gives a user-friendly access to two phylogenetic-based methods implementing the Coev model: the evaluation of coevolving scores and the simulation of coevolving positions. We have also extended the capabilities of the Coev model to allow for the generalization of the alphabet used in the Markov model, which can now analyse both nucleotide and amino acid data sets. The simulation of coevolving positions is novel and builds upon the developments of the Coev model. It allows user to simulate pairs of dependent nucleotide or amino acid positions.
  
  
  CONCLUSIONS
  The main focus of our paper is the new simulation method we present for coevolving positions. The implementation of this method is embedded within the web platform Coev-web that is freely accessible at http://coev.vital-it.ch/, and was tested in most modern web browsers.
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland. linda.dib@unil.ch.|SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland. linda.dib@unil.ch.|Laboratoire de recherche en neuroimagerie, CHUV, Lausanne, 1011, Switzerland. linda.dib@unil.ch.
authors.forename: Linda
authors.initials: L
authors.lastname: Dib
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland. xavier.meyer@iphc.cnrs.fr.|SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland. xavier.meyer@iphc.cnrs.fr.|Computer Science department, University of Geneva, Carouge, 1227, Switzerland. xavier.meyer@iphc.cnrs.fr.
authors.forename: Xavier
authors.initials: X
authors.lastname: Meyer
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland. Panu.Artimo@isb-sib.ch.
authors.forename: Panu
authors.initials: P
authors.lastname: Artimo
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland. Vassilios.Ioannidis@isb-sib.ch.
authors.forename: Vassilios
authors.initials: V
authors.lastname: Ioannidis
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland. Heinz.Stockinger@isb-sib.ch.
authors.forename: Heinz
authors.initials: H
authors.lastname: Stockinger
authors.affiliation: Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland. nicolas.salamin@unil.ch.|SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland. nicolas.salamin@unil.ch.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Salamin
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000378:metabolism*; D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D006801:Humans; D020407:Internet; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D000596:Amino Acids