The problem is it doesn't seem to work anymore!
Why? Simply because Firefox 52 now blocks every plugins except Flash:
Here is a solution to allow Firefox to use others plugins than Flash:
1) Go to main menu Apple -> System Preferences, then Java (very bottom).
Then go to Security panel, and add the url http://www.phylowidget.org/ to the Exception Site list.
Here is my parameters:
2) In the Firefox title bar, write:
=> select: I accept the risk!
3) To the very right of the list, do right-click and select:
Then write: plugin.load_flash_only
And set it to "false".
4) Restart Firefox and finally go again to Phylowidget (http://www.phylowidget.org/).
Now it should work. And this should be similar step with any other java applet, such Jalview (http://jalview.org/).