Why are the applets of Archaeopteryx missing the menus “File” and “Analysis”?

The reason for the absence in the applets of the functionality found in the “File” and “Analysis” menus of the Archaeopteryx application are the security restrictions that are imposed on unsigned applets — for example, unsigned applets are not allowed to access the user’s file system and they are not allowed to print.

More information is available here.

Most the functions in the “Analysis” menu require to load an additional species tree, again something which unsigned applets are not allowed to do.

At this point I unfortunately do not have the resources to develop a “workaround” for these issues.