documentation updates to Align package

reformatted the Align package’s docstrings from epytext to
reStructuredText
seq documentation finished

updated seq module docstrings to reStructuredText format
more documentation updates

monday night update to documentation from epytext to reStructuredText
finalized restructured text format

completed reStructuredText format for all docstrings (detected by
grep), now to clean up errors
restructured text progress

approx. 1/6 done
restructured text progress 2
restructured text progress 3
restructured text progress 4

update 4/6
restructured text progress 5

update 5/6
finished solving reST warnings in docstrings
fixed docstring tests
fixed more doctest problems
Fix rst indentation error; Use embedded URLs for nicer raw view
explicit docformat definitions
Use RST for Bio.CAPS; Include DOI link to paper.
Fix epydoc reStructuredText warning.

$ epydoc -v -o ~/api -u http://biopython.org -n Biopython --docformat plaintext Bio/ExPASy/
+------------------------------------------------------------------------------------------------------------------------------------------------
| File /mnt/shared/users/pc40583/repositories/biopython/Bio/ExPASy/Prosite.py, line 60, in Bio.ExPASy.Prosite.Record
|   Warning: Line 112: Inline interpreted text or phrase reference start-string without end-string.
|
Use literal blocks for code snippets; fix RST warnings

$ epydoc -v -o ~/api -u http://biopython.org -n Biopython --docformat plaintext Bio/Sequencing
+------------------------------------------------------------------------------------------------------------------------------------------------
| File /mnt/shared/users/pc40583/repositories/biopython/Bio/Sequencing/Ace.py, line 5, in Bio.Sequencing.Ace
|   Warning: Line 40: Enumerated list start value not ordinal-1: 2 (ordinal 2)
|   Warning: Line 45: Unexpected indentation.
|
+------------------------------------------------------------------------------------------------------------------------------------------------
| File /mnt/shared/users/pc40583/repositories/biopython/Bio/Sequencing/Ace.py, line 256, in Bio.Sequencing.Ace.parse
|   Warning: Line 264: Unexpected indentation.
|
Use literal blocks for code snippet (and fix epydoc RST warning)

$ epydoc -v -o ~/api -u http://biopython.org -n Biopython --docformat plaintext Bio/SeqIO/Interfaces.py
+------------------------------------------------------------------------------------------------------------------------------------------------
| File /mnt/shared/users/pc40583/repositories/biopython/Bio/SeqIO/Interfaces.py, line 65, in Bio.SeqIO.Interfaces.SequenceIterator.__iter__
|   Warning: Line 73: Unexpected indentation.
|
Avoid lots of epydoc RST warnings, treat as literal block
Fix epydoc RST warning due to underscore.

$ epydoc -v -o ~/api -u http://biopython.org -n Biopython Bio/SCOP/__init__.py
+------------------------------------------------------------------------------------------------------------------------------------------------
| File /mnt/shared/users/pc40583/repositories/biopython/Bio/SCOP/__init__.py, line 619, in Bio.SCOP.Domain
|   Warning: Line 622: Unknown target name: d5hbib.
|