Prank wrapper: added versions to option docs for -(show|no)(xml|tree) change

Their wiki says the change occurred at version 120626:
http://code.google.com/p/prank-msa/wiki/NewFeatures?tm=6
test_Prank_tool: handle Prank's new stdout logging style

Old Prank output:

PRANK: converting 'Quality/example.fasta' to 'temp with space.fas'

New Prank output:

-----------------
 PRANK v.130820:
-----------------

Input for the analysis
 - converting 'Quality/example.fasta' to 'temp with space.fas'
test_Prank_tool: find ".best.nex" output file from the latest Prank

In yet another twist, the latest version of Prank names its output files
"*.best.nex", "*.best.fas", etc. instead of the established "*.2.nex" which the
unittest expected. The unittest now checks for both extensions.