fix bug in _parse_tag_data

the test elem_code == 19 was incorect
Thank Bertrand Néron for ABI fix
BLAST 2.2.28+ added -comp_based_stats and -use_sw_tback to rpsblast
Avoid warning about C Python 3.3.1 if using PyPy3
Remove file after closing subprocess

Was failing under PyPy3 v2.1 on Windows XP
(You can't delete a file on Windows with an open handle)
Don't skip this test under PyPy3
test_phyml_tool: correctly test for presence of PhyML executable

Seems to work with PhyML 3.1 (20120412, currently on their website) and 3.0
(20111216, as packaged for Ubuntu 13.04).

The output of 'phyml --version' doesn't print a semantic version number for
either of these, but always prints a date-stamp in YYYYMMDD format, so this fix
should be OK for the next 86 years.
Cope with Debian naming of rpsblast+ binary
Silence a warning testing with older BLAST+
Update URL for Mark Beaumont's FDist etc
Added options recognized by the XXmotif wrapper script.

This allows using not only the XXmotif binary directly, but also indirectly
through the wrapper.
Import the correct, non-deprecated Bio.motifs.applications wrappers in doctests.
Switches need an alias for use as a Python property/argument name
Clarify docstrings in Bio.Application

No code changes, skip TravisCI testing [ci skip]
PDBParser blank occupancy as 1
Handle blank lines in DSSP (closes Redmine 3441)
Improve assignment of PDB atom element from name.

Previously, hydrogens with a leading digit were given element ""
Test that PDBParser assigns "HE21" as a hydrogen
Also testing under PyPy 2.1 now.

Documentation change only, skip TravisCI tests [ci skip]
Some updates for Bio.motifs.jaspar