8.5. Plug-ins and Applets

If you click on the right click to save locally button in a program output page or on the View button in the Project Management page then some types of files will be sent to the WWW client with a MIME label attached. This allows you to automatically open the file with an appropriate viewer functioning as plug-in of your WWW client. The provided plug-ins are shown (Table 8.1, “Plug-ins and Applets”).

Table 8.1. Plug-ins and Applets
File typeFile name extensionMIME labelRecommended plug-in
lav file, as made optionally by esim4_lavchemical/x-aln2LALNVIEW
GCG MSF.msfchemical/msfGeneDoc, SeqPup
tree file in nested parentheses/Newhampshire/Newick format.dnd .ph .phb .treefilechemical/x-newhampshireNJplot, Treeview
tree file in NEXUS format.tre .trebchemical/x-nexusTreeview

You can declare the plug-ins with the menu option Edit/Preferences.../Navigator/Helper Applications in Mozilla SeaMonkey and with File/Preferences.../File types in Opera. With Mozilla Firefox you cannot configure the plug-ins in advance, but the first time you download a file with a MIME type you can choose to Open with/Browse... and check Do this automatically for files like this from now on. MS Internet Explorer cannot be configured for MIME labels, but opens files according to the link between file name extension and application set in the operating system (start the Windows Explorer and use the menu options Tools/Folder Options/File Types).

wEMBOSS also has built-in applets. As explained above you can, in the Project Management page, select a file and an applet and click View with. Currently wEMBOSS contains two applets. Jalview allows to visualize multiple sequence alignments ; it accepts fasta, GCG MSF, CLUSTAL aln, PIR-NBRF and Stockholm format. ATV allows to visualize a phylogenetic tree ; it accepts nested parentheses/Newhampshire/Newick and NEXUS format.