setup.py: require weblogo
Mention test/ in README
README: mention how to run tests
Refactored/implemented pseudocounts across all strategies
Added 'phospho' strategy for modeling Ser/Thr conservation
Implemented PyMOL script generator to display PDB structures
setup.py: updated dependencies, set version to 0.1.0
Merge branch 'master' of github.com:etal/cladecompare

Conflicts:
	setup.py
Added BSD license
Moved cladereport functions to module cladecompare.report
Refactored "strategy" modules; fixed some bugs too
test: run all 3 strategies independently (gtest, urn, jsd)
Implemented single-MSA mode; globally set pseudocount size to 0.5

Square JSD values to amplify values near 0 or 1 so numbers are more in line with
the p-values returned by other strategies. (JSD isn't a p-value, so this is sort
of OK. Anyway, the "pattern" sites for SCTTLRE show up properly now.)
pmlscript: changed colors to make inserts more visible

Apparently 'silver' and 'gray70' are the same color...
Moved functions from main script to new module 'core'
Renamed library to cladecomparelib to avoid name conflict with script
Removing the old cladecompare (library) directory for good
setup.py: added bottle as a dependency
core: renamed function write_report to write_pvalues

To avoid confusion with the HTML report.
Added script cladeweb.py (local web browser UI)