Doc revision.
Fixed a problem with figuring MSA title from filename.
Revised Evol tutorial.
Fixed examples that fail. Added panel1-3 check to make csb.pitt.edu/Evol work.
Fixed symbolic links to tutorial file folders.
Fixed broken download links.
Merged abakan/prody into devel
Proofread ENM and ensemble analysis tutorials
Merged in timlezon/prody (pull request #14)

Proofread ENM and Ensemble tutorials
Fixed a discrepancy in handling external transformation matrices.
Copies of biomolecule building blocks have different segment names.
Revised log messages.
Doc updates.