Add a potential fix for AMPHORA2 newick support; this may be
reverted as the format isn't quite valid newick, but it does
work w/o regres`sion in tests.  Test case also added.

Test case and fix from the blog post of Bill Nelson:
http://wcnjournalclub.blogspot.com/2014/02/getting-amphora2-to-work-with-bioperl.html