CoPAP Logo Co-evolution of Presence-Absence Patterns

CoPAP Source code


The CoPAP web-server is based on a C++ command line program, gainLoss. The gainLoss program analyzes the evolution of phyletic patterns exactly as described for the CoPAP web server (see Overview). When citing the program, please use the same references as for the CoPAP web server.

1. Downloading and compiling the program
2. License
3. Usage
4. User manual

Downloading and compiling the program:
Current version is from April 2012.
For support and questions please email: or


Download and save to your computer the [win32] executable file. This is a simple command line application that may be run from MS-DOS.
See the section below on usage for a list of the program's arguments.


Copyright (C) 2013 Tal Pupko

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see

The gainLoss program receives input parameters using a parameter file called 'paramFile'.

The basic arguments are:

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