Deprecated API

Deprecated Methods
pal.substmodel.SubstitutionModel.getDimension()
            
pal.distance.DistanceMatrix.getIdGroup()
          distance matrix now implements IdGroup 
pal.misc.TimeOrderCharacterData.getIdGroup()
          TimeOrderCharacterData now implements IdGroup 
pal.substmodel.RateMatrix.getRelativeRates()
          try not to use.