FigTree

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.