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Related Experiment Video

Updated: May 10, 2026

The HoneyComb Paradigm for Research on Collective Human Behavior

The HoneyComb Paradigm for Research on Collective Human Behavior

Published on: January 19, 2019

CoPAP: Coevolution of presence-absence patterns.

Ofir Cohen¹, Haim Ashkenazy, Eli Levy Karin

¹Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.

Nucleic Acids Research

|June 11, 2013

Summary

This summary is machine-generated.

CoPAP identifies coevolving genes by analyzing presence-absence patterns in genomes. This method accurately infers biological interactions, outperforming existing tools for evolutionary analysis.

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations

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Area of Science:

Evolutionary biology
Bioinformatics
Genomics

Background:

Phyletic patterns, representing character presence/absence, are crucial for evolutionary analysis.
Observed patterns in genomes result from ancestral gene gain and loss events.
Inferring coevolutionary signals from these patterns is computationally challenging.

Purpose of the Study:

To introduce CoPAP (coevolution of presence-absence patterns), a web server for inferring coevolving characters.
To provide a platform for comparing coevolution detection algorithms using simulated data.
To demonstrate CoPAP's utility in identifying biologically meaningful gene clusters in bacterial genomes.

Main Methods:

Utilizes state-of-the-art probabilistic methodologies for coevolution inference.
Incorporates advanced network analysis and visualization tools.
Employs simulated data with known coevolving and independent sites for performance evaluation.

Main Results:

CoPAP demonstrates superior performance compared to alternative coevolution detection methods.
Analysis of 681 bacterial genomes revealed clusters of coevolving genes.
Detected gene clusters largely correspond to known biosynthesis pathways and cellular modules.

Conclusions:

CoPAP accurately infers coevolutionary relationships from phyletic patterns.
The tool effectively identifies biologically meaningful interactions and modules.
CoPAP offers a valuable resource for evolutionary and systems biology research.