FORESTER - a framework for phylogenomics
Version 1.9 (October 2001)
Copyright (C) 1999-2001 Washington University School of Medicine
and Howard Hughes Medical Institute
All rights reserved
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Changes from version 1.8 to version 1.9
---------------------------------------

o SDIunrooted:  Improved (cleaner code).
                Uses branches (Node-Node) for rerooting
                instead of nodes (or parent branch thereof).


o ATV:          Search functionality added.
                Right mouse click to inspect nodes.



Changes from version 1.7 to version 1.8
---------------------------------------


o SDIunrooted:  Method "fastInfer(Tree,Tree)" added.  

o ATV:          "Order subtrees", "Uncollapse all", and 
                "Collapse to deepest" functionality added.

                Drawing for multifurcated trees without real
                branch lengths improved.

                Trees with collapsed nodes can now be properly saved.

o NHX format:   "Co=" tag for collapsed nodes added.

o Species tree: A species tree covering more species is included 
                ("tree_of_life_bin_1-4.nhx").




Changes from version 1.6 to version 1.7
---------------------------------------

o ATV:          The ATV application ("ATVapp") gains the ability
                to perform SDI related operations on the displayed
                (gene) tree.

                In versions 1.6 and lower, some bootsrap values did
                not associate with the proper branch after
                rerooting. This is now corrected. 

o Tree class    Some unnecessary methods were removed.




Changes from version 1.5 to version 1.6
---------------------------------------


o NHX format:   All data fields going beyond New Hampshire need to be
                bracketed by '[&&NHX' and ']'. ATV can still read trees
                in the previous definition of the NHX format, but the
                output follows the current definition. This is done for
                compatibility reasons with the NEXUS format.
                Comments are now between '[' and ']'.  
      
o SDIdirectory: Version 1.5 did not save the correct tree when 
                writing option used together with minimizing height
                and minimizing sum of duplication or minimizing L.
                (All the numbers in the summary files were correct,
                and versions before 1.5 did not have this problem.)
                This has been corrected in version 1.6.  



Changes from version 1.4 to version 1.5
---------------------------------------

o ATV: Only insignificant changes.

o SDI: Is now "officially" included and documented.



Changes from version 1.3 to version 1.4
---------------------------------------

o ATV: All: Can now display how many times a sequence is orthologous
  (and "super orthologous" -- no duplications on connecting path) 
  towards another one. New NHX tags "O=" and "SO=".

o NHX: "Seq X branch" data is not being supported anymore.
  NHX tag "Bp=" is deprecated.

o ATV: AWT version of ATV application (ATVapp_awt) looses ability
  to print. In general, the AWT version of the application is
  not being supported actively anymore, since Java 1.2 is now
  available for all major platforms (in contrast, the AWT applet
  is still being actively supported).



Changes from version 1.2 to version 1.3
---------------------------------------

o ATV: All: Collapsing nodes now results in a actually smaller tree.

o ATV Applet: Save tree on server
  A extended version of the ATV Applet which allows to write
  tree files on the server has been added. This modification has
  been developed by Peter Ernst (P.Ernst@DKFZ-Heidelberg.de).
  
o ATV application: Adjust size of printed tree
  The user can now adjust the size of the printed tree in the
  Swing version of ATV application.

o ATV application: Printing in color.
  The user can now choose between printing in color or
  in b/w in the Swing version of ATV application.



(last modified: 10/04/01)

Christian Zmasek


