Extract the contents of the archive to your hard drive:

• Windows: C:\EcoSim\
• POSIX (Linux, OSX, etc): ~/ecosim/

Create a Desktop shortcut to the shell script for your platform.

• Windows: C:\EcoSim\runEcoSim.bat or C:\EcoSim\runEcoSim.vbs
• POSIX (Linux, OSX, etc): ~/ecosim/runEcoSim.sh

A Java 7 Runtime Environment (JRE) is required to execute this program. You can download it here:

http://java.sun.com/javase/downloads/index.jsp

The NJplot executable must be accessible via your system's PATH, or in the EcoSim directory. You can download it here:

http://pbil.univ-lyon1.fr/software/njplot.html

The PHYLIP executable must be in your system's PATH, or in the EcoSim directory. You can download it here:

http://www.phylip.com/

To compile the Fortran programs, you will need to have a Fortran compiler installed. You can download and get installation instructions for the GNU Fortran compiler here:

http://gcc.gnu.org/install/

To compile the Java portion of the program, you will need to have the Java 6 Development Kit (JDK) installed. You can download the JDK here:

http://java.sun.com/javase/downloads/index.jsp

You will also need to have Apache Ant installed for the compilation of the Java program. You can get installation instructions and download binaries here:

http://ant.apache.org/manual/install.html

The Makefile was created to compile these programs in a POSIX environment with access to the GNU Make system. If you wish to compile these programs in a Windows environment using the provided Makefile, you will need to install GNU Make and GNU CoreUtils in addition to the other requirements. You can download the binaries here:

http://gnuwin32.sourceforge.net/packages.html

Cygwin is also an acceptable POSIX environment for Windows. You can get installation instructions, and download the binaries here:

http://cygwin.com/install.html

You will also need to have the Pthreads-w32 library installed. You can get installation instructions, and download the binaries here:

http://sourceware.org/pthreads-win32/

To build the binary files, and create the jar, issue the command:

    make

To build just the Fortran source files, issue the command:

    make fortran

To build just the Java source files, issue the command:

    make java

To clean the directory, issue the command:

    make clean