Avoid odd coloring & trailing blank line in console snippets

Using bash as the language in lstlisting colours keywords like 'for'
and lines starting with '#' as presumed comments within a shell script.

Indenting the \end{lstlisting} was causing a trailing blank line.
Fixed some LaTeX quote markup
Tweak display of Glimmer & Prodigal examples (and tested them)
Fixed quotes, listing trailing blank line, trailing white space
Just keep using the same directory for BLAST part
Be consistent and use *.tab for tabular BLAST output
Tweak (and test) ACT section
Tweaks to MUMmer section etc
Protect single quotes in code listings (for copy & pasting examples)
Merge pull request #3 from peterjc/tweaking

Tweaking