test_Fasttree_tool: Don't use out= option (-out flag) in commands

Older versions of FastTree don't have the -out option, but work with the wrapper
otherwise. This change lets the test pass on more platforms where the wrapper is
usable.

Also cleaned up some extraneous whitespace and PEP8 issues.
test_Prank_tool: removed uses of -noxml and -notree options

These options no longer exist in Prank. Instead, "no" is now the default, and
-showxml and -showtree are available options.
Update ClustalOmega wrapper for software version 1.2.0.