Windows download and installation

   Windows

  1. Disable all antivirus software on your computer. Download the file Workbench_windows_2_0.exe. Double-click this file to extract the contents.

  2. After extraction double-click on “SNAP Workbench Installer” to start the installer application. If installing on Vista right-click the installer and select "Run as Administrator".

  3. Press next on the welcome screen.

  4. Accept the license agreement and press next. Select the location where you want SNAP Workbench to be installed. In most cases the default setting, “C:\Program Files\SNAP Workbench” folder, should be fine.

  5. During installation the Workbench installer will begin installing some additional packages. Ghostscript and Ghostview work together to allow SNAP Workbench to read and display, respectively, Postscript files. If you already have these packages installed on your computer you may cancel the Ghostscript and Ghostview installers and continue on with the SNAP Workbench installation.

  6. The first helper package is Ghostscript. All the default settings for the Ghostscript installer should be fine; the default Ghostscript install location is “C:\gs” and it requires 10-20MB to install. You will needadministrative access on the computer you are installing the workbench to properly install these helper applications.

  7. The second helper package is Ghostview. If you do not see the Ghostview installer window you may need to bring the window to the front by clicking its tab in the Start Bar “WinZip Self-Extractor”. This install will require 7MB of disk space and it will be installed in the default directory “C:\Program Files\Ghostgum”. Click “next” for the next five successive screens, wait for the install to finish and press “Exit” at the “Install Successful” screen.

  8. Installation continues with BioEdit, Graphviz, Inkscape and TreeView. BioEdit will be used for viewing and editing multiple DNA sequence alignments, Graphviz for drawing ancestral recombination graphs (ARGs) as well as phylogenetic networks, and Inkscape for viewing and editing SVG files. The final helper package TreeView allows you to visualize phylogenies.

  9. When the installation is complete switch back to the SNAP Workbench installer and press finish to close the installer. If installing on Vista you will need to right-click the Workbench program and select "Run as Administrator".

  10. Click OK in the Project Gallery window to open the CHV1 project. This is a subset of the data in Carbone et al., 2004 (Carbone, I., Y. Liu, B. I. Hillman and M. G. Milgroom (2004) Recombination and migration of Cryphonectria hypovirus 1 as inferred from gene genealogies and the coalescent. Genetics 166, 1611-1629). Return to the SNAP Workbench folder located in“C:\Program Files\" and open the CHV1_README file in the "Documentation" folder. ** Before proceeding, make sure that you have set extensions to display in Windows 2000 or XP. To do this, open any folder (e.g. "My Computer" or "My Documents"). Then select "Tools | Folder Options", select the "View" tab and scroll down to the entry that says "Hide file extensions for known file types" and make certain it's not checked. Click on the "Apply To All Folders" button and then close the window. ** Follow the steps in the example to familiarize yourself with some of the features and programs in SNAP Workbench.