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
4. User manual
Downloading and compiling the program:
Current version is from April 2012.
For support and questions please email: email@example.com
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.
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:
This will create the following directories:
tar -xvf gainLoss.tar
3. You may use the Make-files to compile the program. You first make the phylogeny library and then 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:
In order to run the second Makefile -
First,to get to the gainLoss directory. Type:
This will result in an executable file called gainLoss, which will reside in the src/gainLoss directory
4. In some systems, the makefiles will not be
operable. Thus, follow steps 1-2 and compile
directly using g++:
cd to the library where you unzipped the files.
mv libs/phylogeny/* programs/gainLoss/
cd to the gainLoss library
To compile, type
g++ -O3 -o gainLoss *.cpp
This will result in an executable file called gainLoss which will reside in the
Copyright (C) 2013 Tal Pupko firstname.lastname@example.org
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/.
The gainLoss program receives input parameters using a parameter file called 'paramFile'.
The basic arguments are:
_performParametricBootstapCorrelation 1 run-type: perform co-evolutionary analysis.
To the top
_seqFile The phyletic pattern data (FASTA format). See the overview section for more details
_treeFile the species tree file name (Newick format). Note: preferable but not essential.