		CHANGES IN PHANGORN VERSION 0.0-4


NEW FEATURES

    o splitsNetwork fits a phylogenetic network using a L1 penalty. 
    
      (High memory consumption)  

    o pmlPen: A new function to estimate penalized likelihood models
    
      for sets of edge weights in mixtures or partition models.

BUG FIXES

    o dist.ml should be more forgiving for different inputs.
    
OTHER CHANGES    
    
    o a new dataset.     
      
      
      

		CHANGES IN PHANGORN VERSION 0.0-3


NEW FEATURES

    o amino acid models 

    o several new maximum likelihood models:
    
      mixture models (pmlMix), and some model for 
      
      phylogenomic data partition models (pmlPart), 
      
      and clustering of partitions / genes (pmlCluster)  
      
      (still experimental, feed back wellcome)
        
    o design matrices for phylogenetic distance methods 
    
    o added some functions useful for simulations
    
      (nni, allTrees) 
    
        
       
    
OTHER CHANGES    
    
    o the data object phyDat changed slightly internally
    
    o a new dataset 
    
    o read.aa to read amino acid data in phylip format 
      
      based on read.dna from the ape package
       

      
      

		CHANGES IN PHANGORN VERSION 0.0-2


NEW FEATURES

    o more generic functions (plot.pml, update.pml) 
      
            
BUG FIXES

    o the "Fitch" algorithm in parsimony contained a bug 
    
    
OTHER CHANGES    
    
    o pml has a cleaner interface (less parameter)
    
    o new faster parsimony analysis (more compiled C-Code) 
          
    o added NAMESPACE
    
          

      
               