New tree manipulation program.

Andrew Rambaut andrew.rambaut at zoo.ox.ac.uk
Tue Jan 4 12:58:51 EST 2000


I would like to announce the first, highly preliminary, alpha version
of my new tree manipulation package. TreeEdit is an application for
organising, viewing and manipulating sets of phylogenetic trees. It is
intended as a tool for preparing sets of trees for use in phylogenetics
packages such as PAUP. 

Runs on Macintosh (PowerMacs) under MacOS 8.5 or above (actually
only tested on 8.5 and above may work on previous systems).

<http://evolve.zoo.ox.ac.uk/TreeEdit/TreeEdit.html>

Features

*  The import and export of trees in a range of commonly used formats.
These include PHYLIP (NEWICK), NEXUS (PAUP and MacClade) and CAIC
formats. 
*  Full drag-and-drop of trees between windows, to the desktop as a
"clipping" or to text editors. In the case of the latter two options,
the trees are written as a NEXUS file. 
*  Cut and Pasting of trees between TreeEdit and text editors (again
the trees are written as a NEXUS file). They can be pasted directly
into PAUP. 
*  Root the tree by clicking on the branch (or node) on which you wish
the root to lie. Midpoint rooting is also available. 
*  Include and exclude taxa or clades. Excluded branches are drawn as
"greyed-out" or can be hidden altogether. Trees can be written without
the excluded taxa. 
*  Edit taxon labels. 
*  Rotate branch order at a node. 
*  Drag and drop editing of branches. 
*  Collapse branches to produce polytomies. 
*  Randomly resolve polytomies. 
*  A set of trees can be "linked" so that an operation done on one is
performed on all the others (if possible). This option is limited to a
few operations at present. 


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The following features are still to be implemented:


*  Er.. lots - please feel free to suggest some more. 
*  The name might even be improved.

------------------------------------------------------------------------

Andrew





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