CHANGES IN PHANGORN VERSION 0.99-3

		
BUG FIXES

    o RF.dist sometimes returned wrong distances
    
    o rate parameter is now properly normalized in pml.Part 
    
      and pmlCluster
    
    o simSeq had problems simulating a single character 
        
NEW FEATURES

    o rSPR and rNNI to simulate tree rearrangements

                    
   
		CHANGES IN PHANGORN VERSION 0.99-2


NEW FEATURES

    o bootstrap.pml and bootstrap.phyDat: parametric 
    
      bootstrap methods

    o simSeq: A new function to simulate sequence data 

    o read.phyDat: simplifies reading in alignments
    
    o SH.test: Shimodaira-Hasegawa test
    
    o RF.dist: Robinson-Foulds distance as replacement 
    
      for treedist (uses less memory and is much faster)
          
BUG FIXES

    o dist.ml returned wrong variances.   
    
    o as.character.phyDat, as.data.frame caused an error 
       
      for alignments with only one site.    
          
OTHER CHANGES    
    
    o added vignette describing how to perform some
    
      standard phylogenetic analysis with phangorn.   
      
    o more functions to convert between different data formats.
    
    o NNI tree search is now general possible for 
      
      partition models (pmlPart, pmlCluster)
        
      

		CHANGES IN PHANGORN VERSION 0.0-5


BUG FIXES

    o Solved a namespace problem with ape (>=2.2-3). 



		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