FigTree v1.

4 2006-2012
Andrew Rambaut
Institute of Evolutionary Biology
University of Edinburgh
a.rambaut@ed.ac.uk
UNIX/Linux/Mac OS X (command-line) version README
Last updated: a.rambaut@ed.ac.uk - 8th October 2012
Contents:
1) INTRODUCTION
2) VERSION HISTORY
3) INSTALLATION
4) OPENING TREES
5) USING FIGTREE
6) EXPORTING RESULTS
7) SUPPORT & LINKS
8) ACKNOWLEDGMENTS
___________________________________________________________________________
1) INTRODUCTION
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 wr
itten for my own needs so may not be as polished and feature-complete as a comme
rcial program. On the other hand, I don't think there are any commercial tree dr
awing programs.
___________________________________________________________________________
2) VERSION HISTORY
v1.4 Released 8th October 2012.
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 attrib
ute/colour scheme being used.
New colour scheme for discrete attributes based on a HSB colour wheel. T
his replaces the old fixed sequence of colours and is more customizable. Attribu
te values can be re-ordered.
New colour scheme for continuous attributes also based on HSB. The old i
nterpolating colour scheme is still available.
Colour schemes are now selectable for particular attributes and these ar
e saved and loaded in FigTree files.
Numerous tweaks to the controls to make things more convenient. These in
clude the reintroduction of font size spinners (in addition to font selection di
alogs) 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 z
oom in. Also added a non-linearity to zooming (starts slower).

Bug Fixes:
Issue
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Issue
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Significant figure spinners don't currently have an effe

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Preference fonts initially set to first font in list

Problem with MidPoint rooting a tree
Taxon labels not displaying traits of nodes
Nexus importer doesn't ignore unrecognised commands
Collapsed clades are clipped at the top of the page
Rerooting doesn't always work.

v1.3.1 Released 21st December 2009.

Bug Fixes:
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).
v1.3 Released 14th December 2009.
New Features:
Added a 'Background' colouring option to the 'Appearance' panel so the c
olour under each clade can be controlled by an attribute.
Added a 'Color by' option to tip, node and branch labels so the colour o
f 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 setti
ngs (it should produce a PDF that matches the screen image).
Implemented a 'QuickLook' plugin for Mac OS X.
Bug Fixes:
Fixed an issue with 'branch' attributes not being loaded from a NEXUS fi
le.
The tree panel now has focus when the window opens which allows direct c
opy/pasting of tree files.
New attributes are available in the Find panel.
v1.2.3 Released 10th Aug 2009.
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 sett
ings.
Bug Fixes:
The scale grid lines could be out of alignment with the axis.
Annotation types being defined in the dialog box were not being created.
v1.2.2 Released 24th Feb 2009.
Bug Fixes:

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 p
age.
v1.2.1 Released 9th Jan 2009.
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.
Bug Fixes:
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)
.
v1.2 Released 30th Nov 2008.
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 a
lso 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 me
nu or the find icon in the tool bar.
Font sizes and a few other options can now be set in the 'Preferences' b
ox. These act as defaults for new windows.
Bug Fixes:
Fixed a problem with branch annotations being applied to the wrong branc
hes when the tree is re-rooted.
"Colour By" colours were reversed from those suggested in the Setup dial
og.
The "Colour By" setup didn't work as expected if Auto-Range was turned o
ff.
Made the control palette title bars slightly thinner.
v1.1.2 Released 6th Feb 2008.
New Features:
Added new graphics export formats using the FreeHEP library. This includ
es 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 informat
ive name.
v1.1.1 Released 22nd January 2008.
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 th
e '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).
Bug Fixes:
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 ma
nually re-rootd.
Branch/node label choices were being lost when colouring or annotation t
ools were used.
Removed the ugly icons from the menu options corresponding to toolbar bu
ttons.
v1.1 Released 13th January 2008.
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 t
hat covers the same space as the clade.
Reroot tree - select node and click reroot button in toolbar. Also selec
t '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 ne
gative 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 do
wn the 'Control' key ('Command/Apple' key on a Mac) to change the centre of view
.
Improved Find dialog - can find inequalities for numerical values.

Bug Fixes:
Negative branch lengths are now correctly displayed rather than being tr
ansformed to unit branches.
Many, other bug fixes and improvements.
v1.0 Released 30th October 2006.
First Released Version
___________________________________________________________________________
3) INSTALLATION
FigTree requires a Java Virtual Machine to run. Many systems will already have t
his installed. It requires at least version 1.5 of Java to run. The latest versi
ons of Java can be downloaded from:
<http://java.sun.com/>
If in doubt type "java -version" to see what version of java is installed (or if
it is installed at all).
Mac OS X version 10.4 or better (Tiger) will already have a suitable version of
Java installed. I am sorry but FigTree simply doesn't run on older versions of M
ac OS X.
On Mac OS X and Windows, FigTree is run like any other application - double clic
k on the application icon.
On UNIX/Linux systems, you may be able to double-click on the figtree.jar file o
r execute the "figtree" shell script.
___________________________________________________________________________
4) OPENING TREES
Simply select "Open" from the "File" menu or on Mac, drag a suitable file onto t
he icon in Finder or the Dock. You can also set files with a particular extensio
n (say, ".tree") to open in FigTree as a default by selecting "Get Info", select
ing FigTree as the "Open With" application and then pressing the "Change All" bu
tton.
Trees can be in NEXUS or NEWICK format.
___________________________________________________________________________
5) USING FIGTREE
At present there is no manual for using FigTree. I suggest you simply try playin
g with the various controls and buttons.
___________________________________________________________________________
6) EXPORTING RESULTS
To export the figure for publication or further editing in a graphics package, s
elect "Export PDF" from the file menu to save as a PDF file.
Saving the tree from within FigTree will save in NEXUS format but add special co
mments and a command block which will enable FigTree to keep all the settings an
d annotations made to the tree. Other programs (such as PAUP) should ignore thes

e settings. You can also 'Copy and Paste' the tree into any application that acc
epts text (the result will be a NEXUS format tree file).
___________________________________________________________________________
7) SUPPORT & LINKS
FigTree is a new program and is not complete or bug-free. Please email me to mak
e suggestions or report bugs:
<a.rambaut@ed.ac.uk>
http://tree.bio.ed.ac.uk/
___________________________________________________________________________
8) ACKNOWLEDGMENTS
Thanks to the following for assisting with the creation or testing of FigTree:
Alexei Drummond
Joseph Heled
Philippe Lemey
Tulio de Oliveira
Oliver Pybus
Beth Shapiro
Marc Suchard