Update ClustalOmega wrapper for software version 1.2.0.
Added -showxml and -showtree options to Prank wrapper
Merge branch 'master', remote-tracking branch 'origin'
Downgrade non-null SFF padding error to a warning (issue #219).

Based on a patch from Martin Mokrejs, this allows the
Biopython SFF parser to be used on invalid SFF files
generated by sff-dump.2.1.7 though 2.1.9 when converting
from *.sra files (problem was due to reuse of an output
buffer, fixed in release 2.1.10).

Martin tested this on SRR088820.sff, ERR016587.sff, and
ERR016602.sff from the SRA.
Migrate Bio.Blast.NCBIStandalone under Bio.SearchIO and put deprecation warning
Migrate Bio.ParserSupport under Bio.SearchIO and put deprecation warning
Remove PendingDeprecationWarning from legacy SearchIO modules
Add docstring to SearchIO._legacy
Add Bio.SearchIO._legacy to setup.py