Phylodendron icon tree printer help

Phylodendron as a Web service

Version 0.8 of Phylodendron includes the ability to run as a Web service to draw trees. This lacks many of the features of the interactive application, but offers the basic functions thru an Internet server. This is not a Java applet, but an HTTP server CGI program (server-side application). In this form, Phylodendron can produce Adobe PDF and GIF image maps and other output formats, in different styles, using tree data. This treeprint variant is currently designed to run on Unix servers, under the equivalent of an Apache HTTPd server.

As an option, the multiple sequence alignment program Clustal W can be included as a CGI service. This wil produce tree files for display by Phylodendron from sequence data. Clustal W software is available for non-commercial use at ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/

For HTTP server installation:

  1. Locate a folder inside your server's document path, name it something like treeapp, and move the TreeApp.jar into this folder.

  2. Install treeprint for server .cgi usage, as
    jre -cp TreeApp.jar install app=treeprint
    -- or --
    java -classpath TreeApp.jar:${CLASSPATH} install app=treeprint
    
    Installing produces several files, index.html, sample files, a print form file, and a treeprint.cgi to call the program.

  3. Execute the install-finish.sh script, as sh install-finish.sh

    or do the needed finishing touches to installation, by making the treeprint.cgi script an executable script, as with chmod +x treeprint.cgi.
    and move or symlink the treeprint.cgi into your server's cgi-bin folder.

    Application code is in TreeApp.jar, but the treeprint.cgi is configured to also look for settings in the file rez/Environ.properties.You can edit this file to tune settings to your taste. Note that usually the HTTP server sets some environ variables such as SERVER_HOST which override these. Images and other files in rez/ are used by the html documents.

  4. Configure new mime types, in your HTTP server/conf/mime.types, if needed
    #mimetype                 server suffixes
    ## for tree files 
    biotree/newick	          tree dnd newick
    ## for java jar files 
    file/jar	                jar