The alchemical_analysis.y script has been moved to

https://github.com/MobleyLab/alchemical-analysis

It contains an implementation of the recommended practices for
analyzing alchemical free energy calculations, as described in
Klimovich et al., JCAMD 29:397-411 (2015). This is based on earlier
work illustrating how to apply MBAR to alchemical free energy
calculations (and a comparison with other methods) as in Paliwal and
Shirts, J. Chem. Theory Comp, v. 7, 4115-4134 (2011).

