GLOOME Source code

gainLossProject

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

Overview

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: talp@post.tau.ac.il or ofircohe@post.tau.ac.il

Windows

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.

Unix

A. Use the [unix] excutable. OR
B. Follow these steps to compile the program under unix system:

1. Download the [ProjectCode].
2. In order to unzip and untar the files, please type:


tar -xzvf gainLoss.tar.gz

This will create the following directories:


libs/phylogeny
programs/gainLoss


3. You may use the makefiles to compile the program. You first make the phylogeny liberary and than the program gainLoss. If this does not work, skip to item 4.
Make sure you are in the directory where you unzipped the files, and type:


cd libs/phylogeny

Type:


make

In order to run the second Makefile -
First,to get to the gainLoss directory. Type:


cd ../../programs/gainLoss


Now type:

make

This will result in an executable file called gainLoss which will reside in the programs/gainLoss directory.
4. In some systems, the makefiles will not be operable. Thus, follow steps 1-2 and compile directly using g++:


1. cd to the library where you unzipped the files.
2. Type
   

   mv libs/phylogeny/* programs/gainLoss/

3. cd to the gainLoss library

   cd programs/gainLoss

4. To compile, type
   

   g++ -O3 -o gainLoss *.cpp

This will result in an executable file called gainLoss which will reside in the src/gainLoss directory.

License:
Copyright (C) 2011 Tal Pupko TalP@tauex.tau.ac.il.

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 http://www.gnu.org/licenses/.


Usage
gainLoss used paramFile that contains the arguments.

The basic arguments are:

_seqFile the alignment (one position) file name, where 0 or 1 is specified for each taxa in the species tree and for each position .
_treeFile the species tree file name (Newick format). Note: preferable but not essential.

Citing the program:

• Ofir Cohen, Haim Ashkenazy, Frida Belinky, Dorothée Huchon and Tal Pupko (2010)
  GLOOME: Gain Loss Mapping Engine
  Bioinformatics, 2010 Nov 15;26(22):2914-5; [ABS] [PDF]
  

• Ofir Cohen and Tal Pupko (2010)
  Inference and characterization of horizontally transferred gene families using stochastic mapping.
  Mol Biol Evol, 27:703-713. [ABS] [PDF]

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