FigTree (original) (raw)

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.

Compiled binaries (for Mac, Windows and Linux) are available from the FigTree GitHub repository.

Source code is available from GitHub.

Version History

2018-11-25 - v1.4.4

2016-10-04 - v1.4.3

Bug fixes

New features:

• Node shape option can now show shapes for internal or external nodes or both.
• Copying selected taxon labels when these are selected, subtree when branches are selected.
• Selecting 'reverse axis' should automatically reverse the Time Scale scale factor. Previously the user needed to set this to -1.0.
• When searching for text, scrolls to show highlighted tip.

Bugs fixed:

• Issue 102: Large SVG files from figtree are broken
• Issue 95: Changing the origin value for the Scale Axis does not work
• Issue 94: The trait legend overlaps the tree.
• Issue 93: Command-line PDF/SVG export options not working
• Issue 92: Reading a file with a mix of integer and real node labels causes exception.
• Issue 90: Export picture cuts the top of the higest tip label
• Issue 79: Export of .SVG produces corrupt files

2014-07-09 - v1.4.2

Bug fixes

New features:

• New -url command line option allows reading of trees from URLs in pipelines.

Bugs fixed:

• Issue 76: Scale axis should only show as many decimal places as necessary.
• Issue 75: Export PNG & JPEG produce blank images.
• Issue 64: Putting node bars on translates the tree to the right (now really fixed, I think).

2014-06-14 - v1.4.1

Bug fixes and new features

New features:

• Copy selected subtrees to clipboard as NEXUS format.
• New graphics export options (PDF, SVG, PNG & JPEG).
• Control panel now scrolls and can be resized.

Bugs fixed:

• Issue 23: Find bar opens slowly with big trees.
• Issue 28: Filtering should work on currently display labels.
• Issue 53: Option Tip Labels: "Colour By" does not render Names in colour.
• Issue 57: Midpoint rooting not working correctly.
• Issue 59: Clear Highlighting/Cartoon etc doesn't seem to work on individual branches.
• Issue 62: When all clades are 'collapsed', the top triangle is clipped.
• Issue 64: Putting node bars on translates the tree to the right.
• Issue 69: Import annotation causes crash.

2012-12-05 - v1.4

First new version for 3 years!

New features:

• Added a 'Node Shape' option which can draw circles, squares or diamonds on each node. These can be coloured and sized by attributes.
• Added a 'Legend' option which can produce a colour legend for any attribute/colour scheme being used.
• New colour scheme for discrete attributes based on a HSB colour wheel. This replaces the old fixed sequence of colours and is more customizable. Attribute values can be re-ordered.
• New colour scheme for continuous attributes also based on HSB. The old interpolating colour scheme is still available.
• Colour schemes are now selectable for particular attributes and these are saved and loaded in FigTree files.
• Numerous tweaks to the controls to make things more convenient. These include the reintroduction of font size spinners (in addition to font selection dialogs) and scrolling of the entire control panel when larger than the window.
• New zooming/expansion. The maximum extent of zooming is now proportional to the number of tips in the tree. I.e., the bigger the tree the more you can zoom in. Also added a non-linearity to zooming (starts slower).

Bugs fixed:

• Issue 52: Significant figure spinners don't currently have an effect.
• Issue 51: Preference fonts initially set to first font in list.
• Issue 50: Problem with MidPoint rooting a tree.
• Issue 48: Taxon labels not displaying traits of nodes.
• Issue 45: Nexus importer doesn't ignore unrecognised commands.
• Issue 42: Collapsed clades are clipped at the top of the page.
• Issue 39: Rerooting doesn't always work.

2009-12-21 - v1.3.1

Fixed some bugs introduced in the last version

New features:

Features added in v1.3

• Added a 'Background' colouring option to the 'Appearance' panel so the colour under each clade can be controlled by an attribute.
• Added a 'Color by' option to tip, node and branch labels so the colour of the labels can be controlled by an attribute.
• Restored a Export to PDF option in the File menu. This uses a different library for creating PDFs from the Graphics export and doesn't require any settings (it should produce a PDF that matches the screen image).
• Implemented a 'QuickLook' plugin for Mac OS X. This allows you to view a tree simply by pressing the space bar in Finder (will also automatically produce thumbnails). See readme in folder for installation instructions.

Bugs fixed:

• Re-introduced the graphic export formats that were inadvertently omitted in the previous version.
• Node bar panel now shows available attributes to display (bug introduced in previous version).

Bugs fixed in v1.3

• Fixed an issue with 'branch' attributes not being loaded from a NEXUS file.
• The tree panel now has focus when the window opens which allows direct copy/pasting of tree files.
• New attributes are available in the Find panel.
• Annotation types being defined in the dialog box were not being created.

2009-12-14 - v1.3

New colouring features, export options and a new 'QuickLook' plugin for Macs

New features:

• Added a 'Background' colouring option to the 'Appearance' panel so the colour under each clade can be controlled by an attribute.
• Added a 'Color by' option to tip, node and branch labels so the colour of the labels can be controlled by an attribute.
• Restored a Export to PDF option in the File menu. This uses a different library for creating PDFs from the Graphics export and doesn't require any settings (it should produce a PDF that matches the screen image).
• Implemented a 'QuickLook' plugin for Mac OS X. This allows you to view a tree simply by pressing the space bar in Finder (will also automatically produce thumbnails). See readme in folder for installation instructions.

Bugs fixed:

• Fixed an issue with 'branch' attributes not being loaded from a NEXUS file.
• The tree panel now has focus when the window opens which allows direct copy/pasting of tree files.
• New attributes are available in the Find panel.
• Annotation types being defined in the dialog box were not being created.

2009-08-10 - v1.2.3

A couple of new features and a few bug fixes

New features:

• Added a 'Reverse Axis' option to the Scale Axis settings - this reverses the direction of the scale axis.
• Added an option to turn on and off the grid lines in the Scale Axis settings.

Bugs fixed:

• The scale grid lines could be out of alignment with the axis.
• Annotation types being defined in the dialog box were not being created.

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.