     
    CHANGES IN IPS (FORMERLY: PHYLOCH) VERSION 1.5-7
    
NEW FEATURES
    o The function mafft() received and additional argument
      'options' with can be used to request options such as 
      e.g. --adjustdirection that are not build into the function's
      interface.
      
	o This version includes a new function phylo2mafft() which does 
	  exactly the same thing as the RUBY script newick2mafft.rb on 
	  the MAFFT website 
	  (http://mafft.cbrc.jp/alignment/software/newick2mafft.rb): it
	  it converts a user-defined guide tree into a format readible
	  by MAFFT.
	  
	 o The functions delete.empty.cells() and fillEndsWithN() are now 
	   using Emanuel Paradis bit-level coding for DNA sequences, which 
	   makes them much faster. 
	   
DEPRECATED FEATURES
    o The function c.genes() has been superseeded by the cbind method
      for object of class 'DNAbin' provided in the package ape.
      c.genes() will be removed in one of the following versions.
    
    
    CHANGES IN PHYLOCH VERSION 1.5-6
  	

NEW FEATURES
    o There is a new function fixedFontBinom(), inspired by
      Emmanuel Paradis' fixedFontLabel() function in ape. The
      function turns the tiplabels of a tree into expressions
      and so can accomodate for taxonomic conventions, e.g., 
      italic font for genera and species, the 'times' symbol
      for hybrid taxa and so on.       


      CHANGES IN PHYLOCH VERSION 1.5-5

    o Minor changes and recompilation for R 3.0.1.


      CHANGES IN PHYLOCH VERSION 1.5-4

    o Minor changes.


      CHANGES IN PHYLOCH VERSION 1.5-3
    
    o Minor changes and recompilation for R 3.0.0.		  


      CHANGES IN PHYLOCH VERSION 1.5-2
    
IMPROVED FEATURES
    o box.clades() and box.tips() have been rewritten and work more
      cleanly now. Yet, they still support only directions 
      'rightwards' and 'leftwards' in phylograms. The argument 'align'
      in box.tips() has now an additional possible value ("tipwise"), 
      which now is the default.


      CHANGES IN PHYLOCH VERSION 1.5-1

NEW FEATURES
    o Argument 'quiet' adde to mafft() and c.genes() to be able
      to suppress screen output by both funtions. 


      CHANGES IN PHYLOCH VERSION 1.5-0

BUG FIXES
    o fixNodes() did not work on some ladderized trees. This is
      (hopefully) now fixed, but users are still encouraged to 
      report any peculiarities. A this stage it might still be 
      good to doublecheck if a unknown tree is manipulated for the 
      first time. (Thanks to Ingo Michalak and Johan Nylander for
      bug report.)  

NEW FEATURES
    o This ChangeLog is included.
    o The stratigraphic chart 2012 is provided for axisGeo();
      see ?strat2012 for details. (Thanks to Lars Nauheimer for 
      providing the data frame).