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

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State: Public
Version: Final published version
Serval ID
serval:BIB_1D409FE82F01
Type
Article: article from journal or magazin.
Collection
Publications
Title
Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.
Journal
BMC Bioinformatics
Author(s)
Dib L., Meyer X., Artimo P., Ioannidis V., Stockinger H., Salamin N.
ISSN
1471-2105 (Electronic)
ISSN-L
1471-2105
Publication state
Published
Issued date
2015
Volume
16
Pages
394
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't Publication Status: epublish
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.
Keywords
Algorithms, Amino Acids/metabolism, Bayes Theorem, Computational Biology/methods, Evolution, Molecular, Humans, Internet, Phylogeny, Sequence Analysis, DNA/methods, Software
Pubmed
Web of science
Open Access
Yes
Create date
04/01/2016 10:41
Last modification date
20/08/2019 13:53
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