FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST.

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Version History

2009-02-24 - v1.2.2

A few bug fixes
Bugs fixed:
  • Exported NEWICK trees now have a terminal semi-colon.
  • Text boxes in control panels are now editable again.
  • Polar trees with 'Align Tip Labels' could cause the tree to go off the page.
2009-01-09 - v1.2.1

A few new features and few bug fixes
New features:
  • Taxon, branch and node labels now have a "Font" button which can be used to set the font for these labels.
  • Added a "Gradient" check box to the "Appearance" panel. This will try to produce gradual colour changes on the branches.
Bugs fixed:
  • Fixed a problem reloading trees with integer annotations.
  • 'Preferences' wasn't available on Windows & Linux (it is now in the Edit menu).
  • Now correctly exports trees 'As Displayed' (i.e., rooted or transformed).
2008-11-30 - v1.2

A few new features and many bug fixes
New features:
  • Added a 'highlight' button which provides a block colouring for a clade.
  • Add a continous colour gradient option to the 'Colour By' control in the Appearance panel. Use setup to activate (at present it disables the 'Width By' option.
  • Added a 'Name' annotation that can be used to edit taxon names. It can also be used to name clades (and these are displayed for collapsed clades).
  • Added a new drop down find panel that is activate by Find in the Edit menu or the find icon in the tool bar.
  • Font sizes and a few other options can now be set in the 'Preferences' box. These act as defaults for new windows.
Bugs fixed:
  • Fixed a problem with branch annotations being applied to the wrong branches when the tree is re-rooted.
  • "Colour By" colours were reversed from those suggested in the Setup dialog.
  • The "Colour By" setup didn't work as expected if Auto-Range was turned off.
  • Made the control palette title bars slightly thinner.
2008-02-06 - v1.1.2

More graphics export formats
New features:
  • Added new graphics export formats using the FreeHEP library. This includes SVG, EPS, PDF and EMF along with raster formats such as GIF, PNG etc.
  • If a tree contains 'labels' (numbers such as bootstrap values before the branch length) then the user is given the opportunity to give these an informative name.
Bugs fixed:
  • A few minor bugs fixed.
2008-01-22 - v1.1.1

Minor update fixes a few bugs
New features:
  • Added the ability to format numerical node/branch labels as percentages (and Roman numerals).
  • Added a 'setup' button for the 'Colour by' and 'Width by' controls in the 'Appearance' palette. These allow customization of the colours and line widths.
  • Added hotkeys for menu options.
  • Added direct menu options for midpoint rooting and node orderings (with hotkeys).
Bugs fixed:
  • The filter (the search box on the toolbar) was not respecting the choice made in the popup menu.
  • The search and filtering options were essentially non-functional. These now work as intended.
  • FigTree crashed with an exception when run on certain Linux variants.
  • FigTree crashed when displaying node/branch labels after the tree was manually re-rooted.
  • Branch/node label choices were being lost when colouring or annotation tools were used.
  • Removed the ugly icons from the menu options corresponding to toolbar buttons.
2008-01-13 - v1.1

Major update
New features:
  • Added a collapse and a cartoon button - collapse produces a single taxon that represents the entire collapsed clade whereas cartoon creates a triangle that covers the same space as the clade.
  • Reroot tree - select node and click reroot button in toolbar. Also select 'Midpoint root' in "Trees" control palette.
  • Rotate nodes - select node and click rotate button in toolbar.
  • Rescale trees - use "Time Scale" control palette (scale factor can be negative which reverses the time axis).
  • Scale axis with grid lines - use the "Scale Axis" control palette.
  • 'FishEye' (1-dimensional) zooming - in "Layout" control palette. Hold down the 'Control' key ('Command/Apple' key on a Mac) to change the centre of view.
  • Improved Find dialog - can find inequalities for numerical values.
Bugs fixed:
  • Negative branch lengths are now correctly displayed rather than being transformed to unit branches.
  • Many, other bug fixes and improvements.
2006-11-01 - v1.0

First released version.
Andrew Rambaut, 2007