Helper applications

# Helper applications for Hovergen

The version of Hovergen accessible through WWW-Query uses two helper applications that allow to visualize and to handle the alignments and the phylogenic trees provided with this database. These applications are SeaView (for the alignments) and NJplot (for the phylogenic trees).

The procedure to set up these two applications is the following:

1. Download the binaries corresponding to your platform.

2. Configure your Web browser in a way to make it able to recognize two new MIME-types: chemical/mase and chemical/njplot. For instance, if you use a UNIX machine, modify the `.mailcap` file of your home directory by adding the following lines:

               chemical/mase; seaview -save clustal  %s
               chemical/njplot; njplot %s

3. Then, when you will click on the hypertext links labelled `ALN` or `TREE`, you will access respectively the protein alignment and the tree of the corresponding gene family in Hovergen.

Seaview allows you to edit the alignment and to save it on your disk. Njplot allows you to root the tree and to swap the nodes. You can also save the tree on your local disk in PostScript format in a way to print it on a compatible printer.

Note that if you do not want to install these applications on your computer or if the binary corresponding to your platform is not available, you can still click on the `ALN` and `TREE` links. In this case the corresponding data will be send as text files to your Web browser.