Phylogenetic Tree Editor v1.0 alpha 10
Copyright © 2002, Andrew Rambaut & Mike Charleston
Supported by The Royal Society, The Wellcome Trust (grant 50275) and the BBSRC (grant BIF05332).
Department of Zoology
University of Oxford
South Parks Road
Oxford OX1 3PS, U.K.
This program may be used and distributed freely but only as the original compressed archive file. We wrote this program for our own use so we have mainly included features that we find useful. However, we would be grateful for any comments, suggestions or bug reports.
WARNING - Playing with the Drag-Edit tool near the root of the tree can cause the program to crash. Please use this tool with caution. I will try to fix this problem soon.
There is no manual at present. Experiment with the menu options and email me for help.
4th October 2002,Version 1.0a10
- Fixed problem reading some trees in (when taxon names were in quotes).
- Fixed problem with printing on Mac OS X (branch lengths were missing).
9th August 2002,Version 1.0a9
- It is now a Carbon application that can run on Mac OS X and Max OS 9.x.
- Can write in an XML format.
TreeEdit should run on any Apple PowerMacintosh computer with at least the following specifications: 601 processor or better, System 8.1 or later, 4MB of memory (on top of that used by the operating system). It should run natively on MacOS X beta (actually it doesn't, but it should) and still run happily on Mac OS 8.1 onwards (although for users of MacOS's prior to 9.0, a library called CarbonLib 1.0.4 will be need to be downloaded from Apple). For systems earlier than 8.5, a library called Navigation Services will be required (also from Apple).
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.
Features (new in this version)
- 'Export Info and Stats' option under the 'File' menu writes various stuff about the trees to a file.
- Can scale the sum of the branch lengths to a given value in the 'Scale Tree' option.
- 'View' menu with options for changing how the trees are displayed. Some of these options come from the other menus, some are new. I have included an experimental radial tree drawing option. This is similar to the circular trees in PAUP/MacClade but with branch lengths. Handy for compact viewing of large phylogenies
- The 'View' menu contains commands for moving backwards and forwards through a set of trees. These have keyboard shortcuts.
- Resolve polytomies options now ask for a branch length to use. The default is zero.
- Collapse short branches now asks for the maximum branch length to collapse.
- Will now import a sequence alignment and it will create a star phylogeny with those taxa. This can then be resolved randomly or edited.
- The high quality tree drawing is an experimental option for drawing the tree more smoothly (especially the radial trees). It is currently slow. It does not affect the printing (which should be high quality anyway).
- Printing now keeps the same aspect ratio (width to height ratio) as the tree as it is currently being displayed on the screen. It will then scale the tree to fit the page. Use the 'Scale' option in 'Page Setup' to alter the size that the tree is printed.
- Can now reorder the tips in various ways.
- Export Matrices (under File Menu) - write patristic distances calculated from trees.
- Raise branch lengths to a power (in Transform Branch Lengths command).
- Can transform the branch lengths in various ways (see below).
- More options for scaling the trees.
- Various format specific options for exporting trees.
- Branch length / node height editing working better.
- Branch lengths / node heights now displayed on tree (select the Display button).
- More operations work on linked trees.
- Edit branch lengths or node heights by double-clicking on a node or taxon label.
- Generate random resolutions or random/all possible root positions into new window or file.
- Read and write CAIC format trees (can't read CAIC branch length files at the moment).
- The import and export of trees in a range of commonly used formats. These include PHYLIP (NEWICK), NEXUS (PAUP and MacClade) 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. Hold down the Command Key to drag and drop a tree.
- 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.
Transforming Branch Lengths
Most operations that alter branch lengths (tree scaling, transform branch lengths, editing branch lengths) make a copy of the branch lengths before changing them. These copied and altered branch lengths are referred to as "transformed branch lengths". The branch lengths originally read in are referred to as "user branch lengths". You can switch between the two using the Branch lengths button at the top of the window.
16th May 2001,Version 1.0a8
- New 'Export Info and Stats' option under the 'File' menu writes various stuff about the trees to a file.
- Can now scale the sum of the branch lengths to a given value in the 'Scale Tree' option.
- Better printing of rotated text (thanks to Dave Swofford for some code).
- Fixed problem writing CAIC branch length files (thanks to Nick Isaac for help with this).
- Many others.
24th January 2001, Version 1.0a7 - Fixed bug preventing some unrooted trees loading.
22nd January 2001, Version 1.0a6 - Now CARBONIZED. This means it should run natively on MacOS X beta (actually it doesn't, but it should) and still run happily on Mac OS 8.1 onwards (although some extra libraries will be required - see System Requirements, below). Fixed bugs and added new features
9th August 2000, Version 1.0a4-61 - Few minor fixes for problems with the features introduced in the previous release.
8th August 2000, Version 1.0a4-57 - Can now write patristic matrices (matrices consisting of pairwise pathlengths from tips to tips). Transform Branch Lengths has some new options - multiply branch lengths by factor and raise branch lengths to a power.
25th May 2000, Version 1.0a4-53 - Big update. Lots of new features and bug fixes.
25th Feb 2000, Version 1.0a3-47 - Fixes universal crashing problem. Silly mistake, my fault, sorry.
24th Feb 2000, Version 1.0a3 - Fixes bug with displaying trees on some older Macintoshes. Some crashing fixed.
Version 1.0a2-36 - Bug fix - fixes problem with mislabeling the tips after reading a NEXUS file.
Version 1.0a2 - Slight update - fixes problem reading NEXUS files.
Version 1.0a1-19 - First, highly preliminary, alpha version.
The following features are still to be implemented:
- Some - please feel free to suggest some more.
Modified by: Andrew Rambaut
Modification Date: 22th January 2001