JTreeview
Tancred Frickey, Andrei Lupas
Originally developed at the Max-Planck-Institute for Developmental Biology Tuebingen
Research School of Biological Sciences
Australian National University, Canberra

JTreeview is a Java based tree viewer available HERE.

Introduction:
While sifting through a large number of trees I came across some 'must-have' features I could not find in any of the available tree viewers (or at least those I could install due to dependency problems). After cannibalizing a few older programs of mine I finally came up with a bare bones tree viewer for Newick format trees. The must-have features included editing of names for the nodes in the tree, being able to highlight leaf nodes by regular expression searches (useful if looking for sequence 'X' in a tree with 500 sequences) and the ability to compare the tree with the corresponding alignment. Since then the tree viewer has been extended to include viewing of subtrees, collapsing nodes with bootstrap support below 'x', abstract representation of whole branches of the tree and other features. NOTE: Still under development. Bug-reports, must-have and nice-to-have features are appreciated.

Program:

There is not really much to say about a tree viewing program. It displays trees. In this case the viewer is limited to Newick format (or the custom save format, based on Newick). Trees can be viewed as either rooted or unrooted, rerooted and every node and leaf node names can be highlighted using regular expression searches (red dot in rooted tree). One interesting feature is the ability to load a sequence alignment containing the sequences present in the tree. This allows the user to select a subtree (branch) and examine the alignment of the sequences present in only that branch.