Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree

BMC Bioinformatics

Software

Nicolas Salamin¹  Xavier Meyer²  Linda Dib³  Vassilios Ioannidis⁴  Panu Artimo⁴  Heinz Stockinger⁴ 

[1] Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland;SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland;Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland;SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland;Computer Science department, University of Geneva, 1227, Carouge, Switzerland;Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland;SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland;Laboratoire de recherche en neuroimagerie, CHUV, 1011, Lausanne, Switzerland;SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland;

关键词: Nucleotide;    Amino acid;    Coevolution;    Phylogeny;    Simulator;    Probabilistic;    Web-platform;   

DOI  :  10.1186/s12859-015-0785-8

 received in 2015-05-04, accepted in 2015-10-20,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundAvailable 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.ResultsWe 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© Dib et al. 2015