        CHANGES IN PHANGORN VERSION 1.0-0

        
NEW FEATURES

    o implementation of many nucleotide substitution models 

      (additional general transition models can be defined)

    o new function modelTest, comparison of different phylogenetic model

      with AIC or BIC 

    o Lento plot

    o subset functions for phyDat objects

BUG FIXES

    o an error in pace is fixed 
           
OTHER CHANGES

    o parsimony (fitch and sankoff) can now handle multiPhylo objects

    o splits structure (which is a list of bipartitions), used by lento
    
      and hadamard conjugation  

    o phyDat objects can be more general generated using a contrast
    
      matrix
    


        CHANGES IN PHANGORN VERSION 0.99-6

        
NEW FEATURES

    o pace, extracts the ancestral states of the root of a tree  
  
      using the sankoff algorithm

BUG FIXES

    o fixed a bug in dist.ml (thanks to Emmanuel)

    o fixed a bug introduced to SH.test in 0.99-5
           
OTHER CHANGES

    o fixed several spelling mistakes in the documentation



        CHANGES IN PHANGORN VERSION 0.99-5

        
NEW FEATURES

    o parallel computing via multicore 

      (so far bootstrap.pml, bootstrap.pml profit under linux)

    o compute edge weights for parsimony trees

BUG FIXES

    o optim.pml had problems when 
    
    o as.character converted ?,- wrongly to NA

    o fitch needed binary trees as input, otherwise pscore is

      likely to be wrong (returns now a warning)
      
    o optim.pml had a problem with identical sequences  
           
OTHER CHANGES

    o optim.parsimony returns now a tree with edge weights 
    
    o vignette is enhanced, I fixed some spelling mistakes and added 
  
      some more examples.



        CHANGES IN PHANGORN VERSION 0.99-4

        
NEW FEATURES

    o new generic function unique.phyDat
           
OTHER CHANGES

    o internal data format phyDat changed 
    
      and data are stored more memory efficient
      
      (optim.pml and friends use less memory and may be faster) 
    
        

		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
    
          

      
               
