Installation instructions for the open-source distribution

Before installing Spectral Networks:

• Matlab must be installed before using this package; details on the installation of Matlab can be found on Mathworks website.
• Compiling this package requires a standard C++ compiler - a Makefile is provided for GNU gcc.
• Support for mzXML files requires the Xerces-C library. Runtime binaries can be downloaded from the Xerces stable distribution.

Installing Spectral Networks

1. Edit the Makefile and change XERCES_ROOT to the directory where you installed the runtime binaries for Xerces-C. Also change CC if you're using a different compiler.
2. Run make
3. Add the Spectral Networks directory to Matlab's search path:
   • In Windows, choose the menu item "Set Path..." from the "File" menu.
   • In Unix, edit (or create) your startup.m file and use addpath.

Optional third-party software

• The recovered spectral networks can be visualized using Graphviz, an open-source visualization tool available here. See the Results section for details on where to find the spectral networks graph files.