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Coev-web: a web platform designed to simulate and evaluate coevolving positions along a phylogenetic tree.
Linda Dib1,2,3, Xavier Meyer4,5,6, Panu Artimo7
1Department of Ecology and Evolution, University of Lausanne, Lausanne, 1015, Switzerland. linda.dib@unil.ch.
BMC Bioinformatics
|November 25, 2015
Summary
This study introduces a novel web platform for simulating coevolving nucleotide and amino acid positions, crucial for evaluating methods that detect correlated evolutionary changes. The Coev-web platform enhances phylogenetic analyses by enabling the simulation of dependent sequence positions.
Area of Science:
- Bioinformatics
- Computational Biology
- Evolutionary Biology
Background:
- Current methods for simulating sequence data often use independent position modeling.
- These independent models are insufficient for assessing methods that identify coevolving positions.
Purpose of the Study:
- To develop a user-friendly platform for simulating coevolving nucleotide and amino acid positions.
- To provide tools for evaluating coevolving scores and simulating dependent sequence data.
Main Methods:
- Development of a web-based platform (Coev-web) implementing the Coev model.
- Extension of the Coev model to generalize the alphabet for nucleotide and amino acid data.
- Implementation of a novel simulation method for pairs of dependent sequence positions.
Main Results:
- A web platform providing access to phylogenetic-based coevolutionary analysis tools.
- The Coev model now supports both nucleotide and amino acid datasets.
- A novel simulation capability for pairs of dependent nucleotide or amino acid positions.
Conclusions:
- The Coev-web platform offers a new simulation method for coevolving positions.
- The platform is freely accessible and supports modern web browsers.
- This tool aids in the assessment of methods analyzing correlated evolutionary changes.
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