PyPy 2.0 has numpy.dot now, but not numpy.linalg
Add comment to tutorial doctest regarding PyPy

No need for TravisCI [ci skip]
One central import for this test
Test Bio.Motif & Bio.motifs PSSM with alternative alphabet.

Addresses this issue: http://www.biostars.org/p/73500/
http://lists.open-bio.org/pipermail/biopython-dev/2013-June/010639.html
Fix motif alphabet instance bug

Previous commit was a test for this bug, addresses
http://www.biostars.org/p/73500/
http://lists.open-bio.org/pipermail/biopython-dev/2013-June/010639.html
Remove now redundant imports
Updating Bio.Entrez DTDs; see bug #3444
Now using GitHub issues not RedMine
Update issue tracker URL in Entrez DTD message
Test EMBL file with missing sequence type in ID line.

Based on a bug report from Peter Thorpe.
Cope with missing sequence type in EMBL
Test EMBL files with missing sequence type in ID line
Fix corner case drawing small JAGGY features on circular diagrams.

The assertion that start <= tail <= head <= end could fail due
to minor floating point calculation differences for tail & head.

Bug report with test case from Peter Thorpe, thank you!
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.