Ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantel’s test, computation of minimum spanning tree, the population parameter theta based on various approaches, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using non-parametric rate smoothing, conversion of APE trees to and from hclust objects and for classifying genes in trees using the Klastorin-Misawa-Tajima approach.
Reference manual pdf 133 pages
Comments: APE  is mostly an environment to develop and implement new analytical methods. It has little capacities for tree manipulations and annotations.

Arbor3D. We adapt the planar tree-of-life metaphor to a virtual, semi-immersive 3D environment. A 3D environment extends the utility of this metaphor by allowing the user to view an entire data set in a single screen. Interrogation of the tree is implemented using 3D input devices. This real-time interrogation of the tree itself provides a quick means by which to qualitatively analyse the hierarchical data. In this paper, we describe the techniques underlying the implementation of such an environment. We conclude by considering the utility of tree metaphors as a basis for the representation of highly dimensional data sets.
Comments: Visualisation only. Requires an immersive display platform

ATV (A Tree Viewer) is a Java tool for the visualization of annotated phylogenetic trees. ATV reads standard "New Hampshire" format tree files (as produced by all major phylogenetic analysis software). ATV also implements an extended superset of New Hampshire format of our own design, called "NHX" format, which allows to extensively annotate a tree (a definition of NHX is available at: http://www.genetics.wustl.edu/eddy/forester/NHX.html). ATV can be used both as application and as Applet. Two versions of ATV exist: One requires Java 2, the other one only requires Java 1.1.x (but has less functions). ATV is part of FORESTER (a framework for automated phylogenomics).
Comments: allows an extended newick format, uses it to find orthologous sequences and gene duplications (using a second species tree).

BAOBAB. Baobab can read Newick, Nexus and XML trees, and write Newick, XML and Pag trees. Tree editor means that it allows you to create and/or modify a tree interactively, adding/(re)moving branches and nodes, changing leave names, setting parameters. Baobab focuses on edition, not representation and display that are only used as a tool to make edition easier. The user can create up to three navigator windows from which almost all edition tasks may be performed. Subtrees displayed in navigators are shown in a distinct color in the control panel. Leaf names can be edited or truncated to a particular size. One can easilly remove some particular characters from leaf names too. Inner nodes may have a name too, which can be use to coerce the underlying subtree. XML files allow the attachment of virtually any kind of data to a tree. Baobab includes an attribute editor that enable the edition of these attributes (see Attributes). Data may be exported for statistical analysis for instance, or even used to color the tree.
Baobab allows you to manage sequence files along with a tree. Supported formats for input and output include Fasta, Mase, Phylip and Clustal. Sequence are stored as attributes, providing their name match the leaf names.
Can save trees as images.
Comments: Simple zooms. Poor annotations capabilities (seemingly under development). Links to sequence file, capable of seaching for ancestral states, manage sequences. Clearly oriented toward phylogenetic analyses. Simple online doc available.

BioNumerics is the only software platform to offer integrated analysis of all major applications in Bioinformatics: 1D electrophoresis gels, all kinds of chromatographic and spectrometric profiles, 2D protein gels, phenotype characters, microarrays, and sequences. The unique power of BioNumerics lies in its ability to combine information from various genomic and phenotypic sources into one global database and conduct conclusive analyses.
Comments: Commercial, not tried. Looks like an integrated tool for the molecular biologist, with no extended capacities for tree manipulation and annotation.

Bosque (means forest in spanish) is a free graphical tool that allows easily to draw, manipulate and prints phylogenetic trees in the newick format, which is the typical output format from phylogenetic programs, such as the ones present on the Phylip package
Comments: requires a C++ Compiler and the Qt package; basic function plus some editing (change labels, fonts...). No real documentation yet.

Compare 2 trees. Software tool for comparing alternative phylogenetic trees. The main application of the software is to compare phylogenies obtained using different phylogenetic methods for some fixed set of species or obtained using different gene sequences from those species. The algorithm pairs up each branch in one phylogeny with a matching branch in the second phylogeny and finds the optimum 1-to-1 map      between branches in the two trees in terms of a topological score. The software enables the user to explore the corresponding mapping between thephylogenies interactively, and clearly highlights those parts of the trees that differ, both in terms of topology and branch length.
Comments: applet available from authors.

DAMBE.Xia, X., and Xie. Z., 2001 DAMBE: Data analysis in molecular biology and evolution. Journal of Heredity 92:371-373.
Comments: for windows. This is an integrated software for molecular phylogeny with basic capabilities for tree edition.
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DendroMaker for Macintosh is a software package for drawing dendrograms on Macintosh computers. DendroMaker can draw and edit bifurcating trees on the screens. The program DM4 is a program for unrooted trees by neighbor-joining (NJ) and maximum likelihood (ML) methods (another program for rooted trees by UPGMA will be available soon). It can read data (tree) files that are written according to the Newick Standard (New Hampshire Format), which is an actual standard for describing trees in text. It can also read data files prepared by using ODEN system (developed by Dr. Y. Ina), which is a program package for molecular evolutionary analyses and is available on 'supernig' of National Institute of Genetics (supernig.nig.ac.jp, Mishima, Japan).
DendroMaker for Macintosh version 4 has been improved on many points in detail. In particular, a function to save trees in PICT files has been added. I hope many researchers make use of the DendroMaker for Macintosh on various aspects of their research activities.
Comments: for the Mac. Basic function, plus some editing, an interesting option: change the proportion of two branches at the root.

DoubleTree, we consider the challenges of visualizing and comparing multiple trees. We extend our work on TaxonTree by developing a new prototype, DoubleTree, which allows users to navigate two trees using coupled interaction. Such an interface not only provides a tool for exploring differences in two similar trees (e.g. two conflicting scientific classifications or phylogenies), but can allownavigation in one tree (e.g. a ‘folk’ classification organized by a non-scientist) to assist information retrieval using  another tree (e.g. a scientific classification).
Comments: DoubleTree is built on TaxonTree, and is dedicated to the comparison of two trees (same restriction as TaxonTree, see below).

DRAWGRAM. Plots rooted phylogenies, cladograms, circular trees and phenograms in a wide variety of user-controllable formats. The program is interactive and allows previewing of the tree on PC, Macintosh, or X Windows screens, or on Tektronix or Digital graphics terminals. Final output can be to a file formatted for one of the drawing programs, for a ray-tracing or VRML browser, or one at can be sent to a laser printer (such as Postscript or PCL-compatible printers), on graphics screens or terminals, on pen plotters or on dot matrix printers capable of graphics.
Comments: historical, was probably the first "good" tree visualisation program.

FORESTER is being developed as a framework for (automated) sequence function prediction based on phylogenic information - phylogenomics. Currently, it is composed of Java classes representing basic data structures, algorithms and tools to operate on phylogenetic trees. For example, it contains an implementation of our speciation - duplication inference algorithm (SDI). It also contains the tree display tool ATV.
Comments: refers to ATV above.

Geneious puts core bioinformatics functions within the reach of all molecular biologists and biochemists in an application that is as easy to use as email.
Geneious does sequence alignment, 3D structure visualization, phylogenetic tree building, sequence analysis, publication-search and more; all in a single application.
Comments: A commercial program for free !

GeneTree is a program for comparing gene and species trees using reconciled trees. The program can compute the cost of embedding a gene tree within a species tree, visually display the location and number of gene duplications and losses, and search for optimal species trees.
Comments: for comparisons of two trees, a species tree and a gene tree and find about duplications, orthologs...
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The H3Viewer library provides layout and interactive navigation of node-link graphs in 3D hyperbolic space. The library can handle quite large graphs of over to 300,000 edges quickly and with minimal visual clutter. The hyperbolic view allows the user to see a great deal of the context around the current focus node.
Comments: initially developed for visualization of graphs derived from a web site. Visualisation only.

Hypergeny is an online tool for viewing large phylogenetic trees. We hope to help researchers visualise and understand large phylogenetic trees by offering a hyperbolic tree browser.
Comments: online and download, visualize and move a tree in hyperbolic context. No annotation, no edition.

HYPERTREE is a phylogenetic tree viewer, with a hyperbolic ('fish-eye') view and editing abilities that help in managing very large trees.
Comments: visualize and move a tree in hyperbolic context. No annotation, no edition.

HyperTree Java Library. The goal of the HyperTree Java Library is to provide a library to ease the implementation of hyperbolic tree visualization.  The hyperbolic tree visualization has been heavily patented by Xerox. So, the use of an hyperbolic implementation, whoever coded it, is illegal in the coutries where the patent applies, if Xerox doesn't gives its agreement. 
Comments: The goal of the HyperTree Java Library is to provide a library to ease the implementation of hyperbolic tree visualization. See also Treemaps.  

MacClade is a computer program for phylogenetic analysis written by David Maddison and Wayne Maddison. Its analytical strength is in studies of character evolution. It also provides many tools for entering and editing data and phylogenies, and for producing tree diagrams and charts.
Comments: commercial. Parsimony oriented,Edit sequences, change tree topology.

Mavric is a python module for the manipulation and visualization of phylogenetic trees. It is also a recursive acronym for Mavric Visualizes Rick's Cladograms :) It aims to be a user-friendly tool for manipulating phylogenetic trees on *NIX-like systems, especially Linux. As such it complements other phylogeny programs like those in the PHYLIP package, which for all their strengths currently lack a nice graphical interface.
Comments: basic functions, edit labels, prune & graft.

MEGA is an integrated tool for automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
Comments: Phylogeny, sequences oriented, a complete software for aligning sequences, phylogeney and making trees, with some capabilities for tree edition.

Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed. 
Comments: phylogeny, sequences oriented, a complete software for aligning sequences, phylogeny and making trees, parsimony oriented, with some capabilities for tree edition (see also Tree Set Viz) such as node naming and annotation, adding web links, pruning and grafting... Export of these trees seem to be limited (the advice is to print and then edit with Illustrator).

MrEnt is a program for drawing high-quality, printable phylogenetic trees. It is a user-friendly software that recognizes Nexus tree files (like those generated by e.g. PAUP and MrBayes) and displays them in the most commonly used tree formats. Our goal was to produce a software to generate with no troubles all tree drawings for scientific publications directly from analysis outputs, without using any additional graphic editor.
Reading of tree files in NEXUS format;
Tree displaying as rectangular cladogram, slanted cladogram or phylogram;
Full editing of taxon names, taxon comments, support values, branches;
Addition of other graphic elements (lines, shapes, text, brackets);
Tree drawing exported as Portable document format (PDF), Windows enhanced metafile (EMF), bitmap (BMP), or Portable network graphics (PNG).
Comments: not tried yet -.NET requirement)

NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
Comments: basic functions, no editing, no annotation.
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PAL (Phylogenetic Analysis Library) is a collection of Java classes for use in molecular evolution and phylogenetics.PAL provides a modular environment for the rapid constructionof both special-purpose and general analysis programs. PALversion 1.1 consists of 145 public classes or interfaces in13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total >of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers.
Comments: A JAVA library of tools. Its is a general package intended to input sequences, calculate a tree and display the tree. The class Package pal.tree, contains functions to move in the tree, manipulate the tree and annotations of nodes and leaves. 2D euclidian representations.
A set of useful functions, no graphical interface.

Paloverde. This is a simple program to do three-D visualizations of moderately large phylogenies. Trees with between 100 and 2500 taxa seem to work best (more if subclades are defined by the user). Faster graphics hardware than is available by default on my Powerbook G4 laptop extend the range upward, as does a large "cinema" display.
The program allows the user to examine the tree from various perspectives and distances. The basic "circle" layout has the most features, but three true 3-D layouts are also available (spiral, cone, and hemispheric, or truly "tree-like"). Several display modes are provided that change the kind of information displayed on large trees, especially with respect to user-defined subclades. These can be defined by the user in the input file, or they can be generated on the fly based on grouping, e.g., all species in the same (monophyletic) "genus" together. Subclades can be displayed as single terminal taxa or they can be displayed in their entirety with visual cues about their membership. A pop-up menu permits the user to select any of these subclades, which are then presented in their own 3D world. Finally, a search tool lets the user zoom to any terminal taxon.
Comments: Visualisation only.

PAUP version 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees, for use in Macintosh, Windows, UNIX/VMS, or DOS-based formats. The influence of high-speed computer analysis of molecular, morphological and/or behavioral data to infer phylogenetic relationships has expanded well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse as conservation biology, ecology, and forensic studies.
Comments:  commercial. Not tried

phpPhylotree is a web application that is able to draw phylogenetic trees. it produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
Comments: no comment yet.

Phylodendron is an application for drawing phylogenetic trees, used in evolutionary biology. Options allow you to save in various formats, print, edit, modify, and adorn the tree.
This version of Phylodendron includes the ability to run as a Web service. 
Comments: dating from 1999, this is probably now outdated (basic functions, some editing).

PhyloDraw support various types of drawings: free tree, radial tree, rooted tree, slanted cladogram, rectangle cladogram, and phylogram, and user can select the tree type interactively. All types of trees don't have edge crossing because they would prevent users from recognizing the phylogenetic information. Beyond PhyloDraw support interactive user editing function: resize the tree, and change the topology of the phylogenetic tree (rooted, unrooted, half-rooted), zoom in/out, etc.,
Comments: also seems to date back from 2000, this is probably now outdated (basic functions, some editing).
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Phylogenetic tree drawing. This is a perl module for reading treefiles in the phylip format and generating PNG files with a graphical representation of the tree. It requires the GD.pm perl module for graphics drawing by Lincoln Stein. There is also an example script demonstrating its use. Click on the figure below to see an example output which makes use of all the features.
The module has a routine called ReadTree which reads the tree into two hash arrays. The first describes the tree by having a key for each node, where the value is the node above it in the tree. The second is the x-axis position of each node which gives the branch lengths.
There is also a drawing routine. In its simplest form the program merely draws a simple tree, with the user specifying the width and size of the image and the branches. It is possible however using hash arrays to specify two widths for each individual branch (one is grey, see example) and also multi-line labels for each node. There is in addition to this an extra label for each final member.
Comments, a perl script to draw a tree in its simplest format.

Phylogenetic Tree Viewer. Visualize the progression of a single DNAml computation over time by stacking up 2D trees (time samples) in the third dimension.  The current version uses the third dimension for easy comparison of any number of tree files.
Comments: visualisation only, the "planes" visualisation is an interesting format. 

PhyloGrapher is a program designed to visualize and study evolutionary relationships within families of homologous genes or proteins (elements). PhyloGrapher is a drawing tool that generates custom graphs for a given set of elements. In general, it is possible to use PhyloGrapher to visualize any type of relations between elements.
Each gene or protein on the PhyloGrapher's graph is represented as a colored node (vertex) and connected to other nodes (vertices) by lines (edges) of variable thickness and color based on the similarity of genes or proteins (distance matrix). The position of each node in the graph is flexible and adjusted by the user to optimize visualization of the inter-relationships between the nodes. Consequently, the physical distances on the graph between nodes have no information content unlike classical phylogenetic trees. The level of similarity between genes or proteins on PhyloGrapher's graphs is indicated by color and line thickness.
Comments: not a tree editor. But I put it here, because I was not sure at first (thanks to François for checkiing), and it may help some people...

Phylomatic is an online phylogenetic query tool where users submit a list of taxa (e.g. from an ecological community), with modern family and genus names, and which returns a phylogenetic hypothesis for the relationships among taxa. Any set of stored phylogenies, or a user-supplied one, can be chosen as the basis for the returned phylogeny, and several output formats for the tree can be selected. Currently, the source databases cover seed plants.
Comments: an interesting approach for people who do not know how to make trees. Could be easily ported to other phylogenies...

Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them. Many distances can be used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored and evaluated according to numerous criteria.
Comments: environment for building trees. Basic options for visualization of trees.

PoInTree (Polar and Interactive Tree) is an application that allows to build, visualize and customize phylogenetic trees in a polar interactive and highly flexible view.
Comments: interesting representation. Allows color coding of leaves according to annotations and sequence management. On the other hand, it builds the tree directly from sequences using NJ algorithm, and does not allow (yet ?) the use specific phylogenetic program. Available on request is described as making use of data stored in an Oracle database (not easy to install... and expensive !).

RadCon is a free phylogenetic tree consensus and comparison program, for the MacOS. Features of note include the strict reduced consensus method, leaf stability, cladistic information content, double decay analysis and matrix representation with parsimony.
Comments: no comment yet.
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SARAGENE.  The analysis of the ever increasing stream of genomics data and the integration of the growing number of biological data sources poses more and more challenges to research in life sciences.This complexity of this problem is increased by the speed with which new data is gathered using automated techniques such as DNA micro arrays. In a joint research project, SARA and the Bioinformatics group at Johnson & Johnson Pharmaceutical Research & Development develop a VR application that offers state of the art data mining capabilities for drug discovery. 3D views in the CAVE™ show hierarchical relationships within gene families, and many to many relationship networks of gene expression data. By integrating data from various databases - location of genes on chromosomes, links/associations with diseases, tissue information – this cutting edge application allows pharmaceutical researchers to achieve their goals: identification of gene functions, of markers for diseases and of new drug targets, more efficiently.
Comments: Commercial product, not tried.

SpaceTree is a novel tree browser that builds on the conventional layout node link diagrams along a single preferred direction. It adds dynamic rescaling of branches of the tree to best fit the available screen space, optimized camera movement, and the use of preview icons summarizing the topology of the branches that cannot be expanded. In addition, it includes integrated search and filter functions. This paper reflects on the evolution of the design and highlights the principles that emerged from it. A controlled experiment showed benefits for navigation tasks to already previously visited nodes and estimation of overall tree topology.
Comments: described as designed to deal with large trees. I was not able to open a tree with the Java Web Start app.

Spectronet is a package for the analysis and visualization of complex evolutionary data that is not best represented by a bifurcating tree. Given an alignment in NEXUS format, the package works by computing a collection of weighted splits or bipartitions of the taxa and then allowing the user to interactively analyze the resulting collection using tools such as Lento-plots and median networks.
Comments: Non tree-like data visualisation.

SpectrumTM is a Macintosh® program designed to read in a data file comprising aligned character arrays (such as DNA sequence data) or distance data in the form of a matrix, and perform some simple spectral analysis procedures on that data. Spectral analysis is a wonderful tool for visualising phylogenetic information without forcing it into a tree - this has the advantage of avoiding (1) the difficulty of choosing which is the "best" method for tree reconstruction, and (2) the whole issue of whether the data is tree-like. .
The program reads in phylogenetic 4-state or binary data, or distance data, and outputs the bipartition spectra corresponding to the data. It can also be used it to find the tree whose expected spectrum is closest to your observed spectrum (the "closest tree" and "Manhattan tree"-- see the manual). Spectrum outputs spectra in Excel format as tab-delimited text files and trees as TreeView files.
Comments: little capability for tree editing, was not written for that.

TaxonTree. we describe our work on visualization techniques that allow effective interaction with vast trees of taxonomic names and associated attributes. Our goal has been to help users find both what theywant and understand the biological context of what they have found. We visualize the tree of names necessary to access further information, thereby creating an innovative portal interface. Our tool provides examples of effective use of techniques, such as animation and zooming of node-link diagrams and integrated searching and browsing. These techniques are well suited generally to tasks that require exploration of large  hierarchically organized biological datasets.
Comments:TaxonTree allows full-text searching and browsing of a large, widely used multimedia database, University of Michigan's Animal Diversity Web via a classification of almost 200,000 animal names. TaxonTree seems to be more dedicated for viewing such tree rather than a powefull tree editor.

THEA. THEA couples a tree to biological knowledge databases (ontologie) such as GO. Althoug designed for exploration of DNA chip data, THEA can be use to explore any tree the leaves of which can be coupled to an ontology. Both manual exploration and statistical analyses are possible.
Comments: No edition, but powerfull tree annotation tool using ontologies.

Treebolic is an applet whose purpose is to give a hyperbolic rendering of hierarchical data.
Comments: takes a tree in XML format. No annotation no manipulation.

TREECON is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences. The evolutionary distance is computed for all pairs of organisms (or sequences) and a phylogenetic tree is inferred by considering the relationship between these distance values. In pairwise distance methods, the dissimilarity (fraction of substitutions) is usually converted into evolutionary distance by correcting for multiple mutations. The most frequently used equations to convert dissimilarities into distances are implemented in TREECON. On the basis of these distances, a phylogenetic tree can be inferred. Different algorithms are available to construct a phylogenetic tree and a few of them are implemented in TREECON. Programs for rooting the unrooted evolutionary trees, for drawing the tree on the screen, and for saving the tree are also included, as well as several other tools. Starting from a simple ASCII text file, containing nucleic acid or amino acid sequences with gaps required for mutual alignment, one can produce publishable trees in a user-friendly and straightforward way.
Comments. Takes sequences and make a tree using various methods. Basic function for tree representation, allows some edition (fonts, colors, colapse, change names).

TreeEdit is an application for organising, viewing and manipulating sets of phylogenetic trees. It is intended as a tool for preparing sets of trees for use in phylogenetics packages such as PAUP.
Comments: includes some editing tools (collapse, taxon edition...).

Tree Draw Deck. A Hypercard stack which draws phylogenetic trees. It is derived from Drawgram and Drawtree
Comments: deprecated.

TreeDyn is a full featured environment for drawing trees, manipulation and annotation.
Comments: TreeDyn includes every tools that tou can find in any other classical (2D euclidian) package, and much more. TreeDyn can manage large trees, many trees, includes export in many format (including "live" html). TreeDyn can manage relationships between trees, annotation and complex edition. It is possible to use annotation files to annotate leaves or node, either manually or through a SQL like langage. Finally (not exactly, TreeDyn includes much more) TreeDyn is scriptable : you can use a script to produce publication ready figures and not bother by doing again and again the same formatting of you trees.
NOTE : now can import treebase trees.

TREEFINDER computes phylogenetic trees from molecular sequences. The program does maximum likelihood phylogeny reconstruction under many models of sequence evolution using nucleotides or amino acids. It can account for rate heterogeneity among sites. Separate models can be assumed for user-defined data partitions, separate rates, separate character compositions, separate weights. All model parameters can be estimated from the data. A fast tree search algorithm allows analysis of large data sets, user-supplied topological constraints may guide the search. The software has been tested extensively.
Comments: takes aligned sequences and compute a ml tree (seems efficient) with plenty of options; only basic tools for tree representation.

TreeGraph assists in producing complex ready-to-publish figures of phylogenetic trees. The TGF format used by the program automates formatting of several different statistical support value types (confidence estimates) per tree node. Moreover, internal text and graphical labels are automatically arranged at the nodes as are annotations for clades or groups of terminals. TREEGRAPH imports NEXUS trees and related file formats. Beyond common tree edit operations, simultaneous pruning of subtrees (simplification of the tree to higher order clades) and saving of subtrees is possible. TREEGRAPH exports to the standard vector graphics formats Scalable Vector Graphics and PostScript.
Comments: A command line oriented package. Some powerful commands to edit and annotate a tree.
NOTE : the "tgf file" format is different from the tgf file format of TreeDyn !

TreeIllustrator is a program for displaying and manipulating phylogenetic trees. It gives you powerful means to customise your phylogenetic trees and compare them with the current classification of organisms.
Handle large trees.
Comments: commercial, part of The SeqPad software suite, not tried.
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TreeJuxtaposer. Compare phylogenetic evolutionary trees interactively and automatically. Uses nested parentheses (Newick/New Hampshire) data format. Guaranteed visibility of marked regions provides visual landmarks.
Structural differences are automatically marked, and the marked clades highlight corresponding nodes on the trees through the use of a generalization of the Robinson-Foulds distance metric.
Draw whole trees in under a second with progressive rendering.
Comments: a tool to compare two trees and find similarities/differences. Minimal documentation and non intuitive software (webstart tried).

Treemap is a space-constrained visualization of hierarchical structures. It is very effective in showing attributes of leaf nodes using size and color coding. Treemap enables users to compare nodes and sub-trees even at varying depth in the tree, and help them spot patterns and exceptions.
Comments: unconventional ! Clearly a different manner to represent trees. No editing or manipulation tools. Makes use of annotation files that contain labels assigned to each leaf of the tree. Color code the "tree" according to these annotations. Finally it is also possible to use some kind of hybrid representation that mix the "tremap" structure with a conventional tree near the root. The tree is displayed mid-rooted.

TreeMe is a comprehensive phylogenetic tree visualization and manipulation software for phylogenetics and research in evolution.
Comments: TreeMe supports so called 'tags' which are an extension to conventional tree formats. These tags include additional information for nodes, clusters or branches. The user-defined tags can be applied to loaded trees if the appropriate identifiers are present in the tree. The tags can define arrows, boxes, rectangles, branch widths, text notes to be optionally shown for individual nodes or clusters. Tags can be included into the tree files during the saving procedure and are then available after reloading of the file. However, these tags cannot be displayed by any other tree visualization software and seemingly not exported as well to html files as in TreeDyn.
Not clear if commercial or not for the full app ?

Treeplot is a conversion tool, from "Phylip" phylogenetic tree file to :
Postscript (.ps), Adobe Illustrator (.ai), Computer Graphic Metafile(.cgm), Hewlet Packard Graphic Language (.hpgl)
xfig file (.fig), gif image file(.gif), PBM Portable aNy Map file (.pnm)
Comments: TreeDyn does more. Besides, the pdf file is easy to do under Linux (try pdfcreator for example, if you use windows), and for producing any of these image format directly from screen, try Gadwin.... May be the color list (but go for TreeDyn).

TreePlus is an interactive graph visualization system based on a tree-style layout. TreePlus transforms graphs into trees and shows the missing graph structure with visualization and interaction techniques. For example, TreePlus previews adjacent nodes, animates change of the tree structure, and gives visual hints about the graph structure. It enables users to start with a specific node and incrementally explore the graph.
Comments: no download page, no documentation.

The Tree Set Visualization program is capable of summarizing large sets of phylogenetic trees. This program depicts a "tree space" using multi-dimensional scaling based on tree-to-tree distance metrics. Visualizing sets of trees in such a way can yield more information about the trees that may otherwise be lost using more conventional methods for condensing large sets of trees.
Comments: this is an application devoted to the analysis (distances between trees) and colouring of trees according to scores (for example to analyse multiple trees produced by parsimony). Most usefull for very precise phylogenetic studies. A companion to Paup and MacClade.

Treetool is an interactive tool for displaying, editing, and printing phylogenetic trees. The tree is displayed visually on screen, in various formats, and the user is able to modify the format, structure, and characteristics of the tree. Trees may be viewed, compared, formatted for printing, constructed from smaller trees, etc...
Comments: developed by RDP (and maintained by) TreeTool includes all basic operations as well as collpase, prune, coloring and some basic editing capabilities.
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 TreeView provides a simple way to view the contents of a NEXUS, PHYLIP, Hennig86, Clustal, or other format tree file. While PAUP and MacClade have excellent tree printing facilities, there may be times you just want to view the trees without having to load the data set they were generated from. The PHYLIP package contains tree drawing programs which offer a greater variety of trees than TreeView, but are somewhat clumsy to use. The forthcoming PAUP* for Windows does not have a graphical interface, hence TreeView allows you to create publication quality trees from PAUP files, either directly, or by generating graphics files for editing by other programs.
The program currently reads trees with up to to 1000 taxa.
Comments: limited to trees with less than 500 nodes and has limited save graphic options (pict and windows metafile); it can plug directly into treebase for importing trees. It includes every basic operation as well as collpase and Ladderize. Does not include extended editing capabilities not annotation tools.

T-Rex is mostly a phylogeny software with some drawing capacities.
Comments: some very interesting implentation of phylogenetic algorithms. In particular makes use of reticulation and can plot it. Very basic tree manipulations only.

TreeWiz is a tool written in JAVA that can be used to show and to interactively explore trees with more than 50000 leaf nodes. The tree file format supported so far is the Newick (New Hampshire) format. Trees of this size are e.g. derived from protein databases by hierarchically clustering of all its elements. There are two versions of TreeWiz: an applet version with restricted capabilities which can also be used to view local tree files (presumed that a local .java.policy file has been changed accordingly) and a Java application. The program is available for free for non-commercial use, subject to our licence.
Comments: TreeWiz was designed for the exploration of very very large trees. It has extended zooming and filtering capabilities. This is however more an exploratory tool than a tree editor, it has poor capabilities for drawing publication ready figures and no annotation capability.

Walrus is a tool for interactively visualizing large directed graphs in three-dimensional space. It is technically possible to display graphs containing a million nodes or more, but visual clutter, occlusion, and other factors can diminish the effectiveness of Walrus as the number of nodes, or the degree of their connectivity, increases. Thus, in practice, Walrus is best suited to visualizing moderately sized graphs that are nearly trees. A graph with a few hundred thousand nodes and only a slightly greater number of links is likely to be comfortable to work with.
Comments: Interesting for visualisation of very very large datasets. Visualisation and navigation only.