Education

Feb 15 2018

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Ed of e

Ed of e

  • 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.
  • 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

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.

Ed of e

Version History

  • 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.
  • 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
  • New -url command line option allows reading of trees from URLs in pipelines.
  • 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).
  • Copy selected subtrees to clipboard as NEXUS format.
  • New graphics export options (PDF, SVG, PNG & JPEG).
  • Control panel now scrolls and can be resized.
  • 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.
  • 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).
  • 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.

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.
  • 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.

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