http://tree.bio.ed.ac.uk/software/figtree/

What is new?
        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.

Bug Fixes:
        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.