      CHANGES in PHANGORN VERSION 2.0-0

NEW FEATURES

    o hclustNNI upgma automatically used improved 

    o NNI now available for pml for rooted trees

    o species tree coalescent models (Rannala & Yang 2003)

BUG FIXES 

    o as.data.frame.phyDat returned only site patterns and so did 

      write.phyDat for nexus files

    o some of the recently introduced (1.7-4) amino acid models were not known by all

      functions and contained NAs (Thanks to JJ )

OTHER CHANGES

    o pmlPart is more flexible and has an additional parameter weight

    o faster code for ML methods with rooted topology

    o improved partition models 

         * easier to set up 
  
         * optimisation of global parameters is much faster       


TODO

upgma NNI

write.data.frame, which affects also write.phyDat
optimEdge incl. partitions 
optimRooted incl. partitions
NNI for rooted and unrooted

NNI and parameter for 

optim.parsimony SPR for fitch as default
pratchet rearrangement=SPR 5 statt 10 als Wert. 

Ziel: 
Partition models 10x faster to model gene trees

