Tutorial/Phylo: mention CDAO support, FastTree wrapper

Suggest DendroPy, PyCogent as other good Python libraries for phylogenetics.
NEWS: mention that there were bug fixes, test improvements since beta.
DSSP test: support more versions.
Fix DSSP changes under Python 2.5 (with statement)
Turn PDB numpy import error into MissingPythonDependencyError

This is an ImportError subclass, so shouldn't break anything.
It has the benefit of making things cleaner in the unit tests,
e.g. test_DSSP_tool.py
Python 3 fix for test_DSSP_tool.py
Fix copy & paste error in last commit.
Version bump for Biopython 1.62 release
Adding a few more contributors to Biopython 1.62
Post release version bump
Update .travis.yml to drop Python 2.5
Remove with_statement imports required under Python 2.5

Removed all the with statement imports
(and any comment lines associated with them);

from __future__ import with_statement
Update setup.py now we've dropped Python 2.5
Start recording contributors to the next release
Use byte literals (new in Python 2.6).

The old constants were defined via our _as_bytes function
in order to work under Python 2.5 as well.
Update DEPRECATED file entry for Python 2.5

Documentation change only, skip TravisCI testing [ci skip]
Changed exceptions to be py3k compatible
Thank Chris Mitchell for his contribution
Update README now that we've dropped Python 2.5
Partially migrated to print-function-like syntax

  For now we only handle the 'print' statement with a single argument,
  i. e.:

      print ... -> print(...)

  Migration was performed using a 2to3 fixer class:

      from lib2to3 import fixer_base, patcomp
      from lib2to3.fixer_util import Name, Call

      parend_expr = patcomp.compile_pattern(
          """atom< '(' [atom|term|testlist_gexp|STRING|NAME] ')' >""")

      class FixSinglePrint(fixer_base.BaseFix):
          PATTERN = "print_stmt"
          BM_compatible = True

          def transform(self, node, results):
              assert results
              assert node.children[0] == Name(u"print")
              args = node.children[1:]
              if len(args) != 1 or parend_expr.match(args[0]):
                  # We only fix 'print' statements which have _exactly_ one
                  # non-parenthesized argument.
                  return

              l_args = [arg.clone() for arg in args]
              l_args[0].prefix = u""
              n_stmt = Call(Name(u"print"), l_args)
              n_stmt.prefix = node.prefix
              return n_stmt