File: helpers.html

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<HEAD>
<TITLE>Helper applications</TITLE>
</HEAD>
<BODY BGCOLOR="#F0F0F0">
<CENTER>
<H1>Helper applications for Hovergen</H1>
</CENTER>
<HR>
<P>
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
<A HREF="/software/seaview.html">SeaView</A> (for the alignments) and
<A HREF="/software/njplot.html">NJplot</A> (for the  phylogenic trees).
<P>
The procedure to set up these two applications is the following:
<OL>
<LI><A HREF="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny">Download</A>
the binaries corresponding to your platform.
<P>
<LI>Configure your Web  browser in a way to make it able to
recognize two new MIME-types: <I><B>chemical/mase</B></I> and
<I><B>chemical/njplot</B></I>. For instance, if you use a UNIX machine,
modify the <CODE>.mailcap</CODE> file of your home directory by adding the
following lines:
<PRE>
        chemical/mase; seaview -save clustal  %s
        chemical/njplot; njplot %s
</PRE>
<LI>Then, when you will click on the hypertext links labelled
<CODE><B>ALN</B></CODE> or <CODE><B>TREE</B></CODE>, you will access
respectively the protein alignment and the tree of the corresponding gene
family in Hovergen.
</OL>
<P>
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.
<P>
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 <CODE><B>ALN</B></CODE> and <CODE><B>TREE</B></CODE> links. In
this case the corresponding data will be send as text files to your Web browser.
<P>
<HR>
<ADDRESS>
<A HREF="/comments.html">If you have problems or comments...</A>
<P>
<A HREF="/pbil.html"><IMG SRC="/binaries/home.gif"></A>
Back to PBIL home page
</BODY>