DistributedRunner - we don't need to keep a list of slaves
Estimator, CoreUtils - minor clean up, add a util method in CoreUtils to print log messages
LikelihoodCalculator - only calculate prior if one has been specified
BranchLengthComparer - add some R code to analyse output
Put processing of checkpoint file in its own class
Checkpoint files output Fitness parameters in canonical amino acid order
Use the ant project for the distribution jar
Fix typo in Estimator
Fix indentation of build.xml
Add functions to PhyloUtils to iterate over a Tree's internal and external nodes. Use this throughout.
Fix project name expansion
getDistinctAminoAcids function simply calls getObservedAminoAcids, and add unobserved amino acids to to the result. (Should probably have a better name)
Move AbstractRunner.getAllResults to CoreUtils.getFutureResults
Display usage if arguments cannot be parsed
Extract a getRunner() method
Minor naming changes
Clean up some redundant code. Reorganise in view of implementing non-homogeneous prior.