This package contains Java classes for the analysis of residue coevolution in proteins.

See:
Description

Packages

org.gersteinlab.coevolution.core.config	Contains classes for configurating the programs.
org.gersteinlab.coevolution.core.data	Contains classes for configurating handling data.
org.gersteinlab.coevolution.core.io	Contains classes for IO operations.
org.gersteinlab.coevolution.core.stat	Contains classes for coevolution score computations.
org.gersteinlab.coevolution.core.tasks	Contains classes that define the main tasks of a coevolution study.
org.gersteinlab.coevolution.core.util	Contains supporting utility classes.
org.gersteinlab.coevolution.inter	Contains classes for performing inter-protein analysis.
org.gersteinlab.coevolution.intra	Contains classes for performing intra-protein analysis.
org.gersteinlab.coevolution.web	Contains classes for performing analysis through the web interface.

This package contains Java classes for the analysis of residue coevolution in proteins. It provides methods for downloading and preprocessing data, computing coevolution scores, and plotting and analyzing results.

There are three ways to use the classes:

• The easiest way is to use the web interface at http://coevolution.gersteinlab.org/, which provides step-by-step guidelines for calling the classes running at a backend server.
• If you need to perform large-scale experiments, it is better to download the codes from the web site and run them locally. Please refer to the installation guide for detailed instructions.
• If you want to use the classes in your own programs, you only need the file WEB-INF/lib/coevolution.jar in the downloaded package. Simply put it in your classpath so that the Java compiler and runtime environment can find it.

This API documentation is mainly for the third group of users, who need to understand how the API is defined and what the classes actually do.