GLOOME Logo Gain Loss Mapping Engine

GLOOME Source code


A C++ shell program for the detection of gain ans loss events


The gainLoss is a program that analyzes the evolution of phyletic patterns within the likelihood framework. The evolutionary model assumes that the gain and loss substitutions follow a Markovian process. The first phase of the analysis is the estimation of the parameters of the underlying model (various models are implemented). The second phase consists of various computations including the computation of the posterior empirical Bayesian expectation of the rate, gain and loss for each position in the phyletic pattern. Finally, the program uses stochastic mapping approach for the estimation of the probability and expectation for the number of events (gains and losses) at each position and each branch.

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

Downloading and compiling the program:
Current version is from May 2013.
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) 2011 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

gainLoss used paramFile that contains the arguments.

The basic arguments are:

Citing the program:
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