Analyze the genome with this tool. AssociationViewer is a Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.

AssociationViewer Features:
1. Display SNPs and their p-values in a genetic context, similar to usual genome browsers
2. Automatically download supplementary information from Ensembl/Biomart
3. Display Hapmap LD plots
4. Print and export the display to various data formats
5. Import external data file such as BED or Wiggle as supplementary tracks
6. Does not require to have a local copy of any data or data source, except for the primary file of SNPs and their respective p-values
7. Users can scroll and browse through their data in real time
8. Small in size (AssociationViewer itself is less than 800 KB, less than 5 MB with the required libraries)
9. Downloaded data is kept in a cache locally for faster access
10. Due to the cache, memory requirement is reasonable

To start AssociationViewer, the easiest and prefered way is to use the Java Web Start link. If you want to start it manually via the command line, you first have to download the application itself, as well as the required libraries (see the download section). Save the application in a safe place, then at the same place create another directory called "lib". Put all the libraries in that directory. When it's done type in a command line:

java -Xmx256M -jar associationviewer.jar

where 256 is the amount of memory in Megabytes reserved for the application. Double-clicking on the associationviewer.jar will start the application with 64 MB of memory, which might be not enough with larger datasets.
1. When using the Java Web Start link, AssociationViewer has to be a signed application, which means that you have to accept the certificate in order to allow it to access your hard disk (for reading and writing).
2. If it is the first time you start the application, it will ask you where to create the directory containing temporary/cached data. Connections to the different data sources used in AssociationViewer are then checked.

Tips & tricks
1. Single-clicking on a track will display details about either the SNPs or the genes at this position in the left panel.
2. Double-clicking on a track will zoom in at this position
3. Regular keyboard shortcuts can be used where tables are used to display data. In the following list, replace META with the appropriate key on your OS (i.e.: CTRL for Windows or Linux).
* META-C copy
* META-V paste
* META-X cut
* META-A select all the elements

4. Both the menu bar and the browser bar can be dragged and dropped outside the AssociationViewer window. Closing these components will put them back at their original location.
5. Tooltips are associated with most of the buttons or graphical components. They appear when one leaves the mouse cursor for a few seconds over a component.
6. To give more space to the tracks, one can click on the little arrow below the chromosomes list (it will collapse), Clicking on the other arrow will bring it back.
7. The main window can be resized.
8. If AssociationViewer is not automatically updated (to check your current version go to Help menu, About entry), you might have to empty the cache of your browser.

Requirements:
* Java

The license of this software is Free, you can free download and free use this cad software.