ArticleBMC bioinformatics2015
Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Duplication history and molecular evolution of the rbcS multigene family in angiosperms.Journal of experimental botany · 2019Article
- Simultaneous Bayesian inference of phylogeny and molecular coevolution.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates.Nucleic acids research · 2019Article
- Polymorphic sites preferentially avoid co-evolving residues in MHC class I proteins.PLoS computational biology · 2018Article
- Selection on the Major Color Gene Melanocortin-1-Receptor Shaped the Evolution of the Melanocortin System Genes.International journal of molecular sciences · 2017Article
- Widespread Historical Contingency in Influenza Viruses.Genetics · 2017Article
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Authors and funding
6 authors.
Funding
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Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.