Trees and Tree - softwares for visualisation and manipulations

Dealing with phylogenetic trees - a "comprehensive list"

Also some additional utiliies

See by category the "best" programs
Submit your software: send a mail christen(replace)unice.fr
Submit a review, changes, suggestions, send mail to adress above
Summary table          Short descriptions   Some repositories   XML   Graphs    Bibliography
back to biodiv outils disponibles (french), and of course see also Joe Felsenstein web page
Introductions to phylogeny:
The complete cladist (American Museum of Natural History): pdf
The PhyloCode  html
The Tree Thinking Group html
Microbial Phylogeny  html1  pdf1
Tree of life  html
Diverse documents : Systematics Taxonomy Mega Yahoo  Google1 Google2 Scirus  NCBI
Find articles using : Jane   eTBlast  PubMed

Summary of available tools. updated 2010/07. Most recent in red

Program web site  update OS comment & clic for a short description manual
3DPE 2007 MS Windows. OSX Python  + VRML2. Some 3D capabilities. PMID   pdf
APE 2004   R package pdf
ARB 2003  Linux Mac OSX  complete environnement  
Arbor3D 2000 SGI immersive 3D  PMID  
Archaeopteryx 2010 all requires Sun Java version 5
ATV 2002  all Java   (now replaced by Archaeopteryx) pdf
BAOBAB 2005  all  JAVA  
Bio::Phylo 2011 all Perl PMID  pdf
Bionumerics     Commercial  
Bosque 2008
 all Integrated programs pdf
Compare 2 trees 2006 applet compare 2 trees pdf
COMPONENT 2001 Windows consensus, comparisons, reconciled trees  
CTree 2007 all analysis of clusters within trees (Java) PMID    pdf 
DAMBE 2001   Windows  
DendroMaker 1998   Mac  
DendroPy 2010 all Python PMID  pdf
Dendroscope 2007 all Display manipulate hudge trees. Java BMC bioinfo
DoubleTree 2003   DoubleTree  
Drawtree all Python, minimalist  
Drawtree and DrawGram...
 1998   included in PHYLIP. Online Drawtree  Drawgram  
ETE 2010 all Python BMC Bioinfo
ExploreTree 2009 all (Java) Used by the phylogenetic tree of life  
FORESTER 2002   Java relies on ATV  
Geneious 2006 all Commercial  
GeneTree 2001 Mac Windows  GeneTree  
GenomeDiagram 2006 all python package, not really a tree viewer PMID  pdf
H3Viewer 2001 all H3Viewer  
Hypergeny     web hyperbolic tree browser  
HyperTree Java 2001   HyperTree Java  
iTOL 2007 web Web based PMID   pdf
jPHYDIT     for rRNA  
K tree score 2007 Compare 2 trees. Perl PMID   pdf
Jstree 2010 all Javastript
HYPERTREE 2004 all Java  
MacClade 2005 Mac Commercial  
Madeline 2.0 2007 all (source code) a new program for local and web-based pedigree drawing (C++) PMID
MAST 2004 all ???. In fact published as "TreeAnalyzer". Java. PMID  
Mavric 2001 all python module  
MEGA 2005 all complete environnement  
Mesquite 2005  all complete environment (uses Tree Set Viz).  
MrEnt 2006 Windows requires .NET Framework 1.1  
NAViGaTOR 2009 all Network Analysis, Visualization and Graphing Toronto PMID
Nexplorer 2006 web web-based PMID   pdf
newicktree 2004 Latex: draw newick in Latex documents or Word PMID   pdf
Newick utilities 2010 Unix shell UNix shell PMID  pdf
NJplot 2008 all Very simple, but powerfull and copy/paste to vector format  
NJplot unrooted     same as NJplot  
PAL 2004 all PAL (JAVA)  
Paloverde 2006 all 3D    C OpenGL PMID  pdf
Panta rhei 2006 Windows, OSX WorkBench  Java (QAlign2) PMID  pdf
PAUP 2001 all Commercial  
phpphylotree
 2005 all web application  
PHY.FI 2006 all Python. Online application pmid   pdf
Phylo-comparison 2005 web web application. Java applet PMID   pdf
Phylodendron 1999 all Java  + web, see also web app  
PhyloDraw 2000 Windows PhyloDraw PMID  pdf
PhyloGena 2007 all Pipeline PMID  pdf
Phylogenetic Tree Drawing 2003 all perl moduleinteractively exploring sets of phylogenetic trees  
Phylogenetic Tree Viewer 2000 IRIX6.5 for dnaml  
PhyloGrapher 2001 all Tcl/Tk  
Phylomatic 2006  web web, and standalone: assembly of the tree-of-trees database  
Phyloview 2006 web server Taxonomic coloring of protein sequences PMID   pdf
Phylo_win 1996 all environnement, uses njplot  
PhyloWidget 2008 web Use web server or download source code help
PHY.FI 2006 fast and easy online creation and manipulation of phylogeny color figures. PMID  
Phyutility 2008 all Java, summarizing and manipulating phylogenetic trees PMID   pdf
PoInTree 2005 Windows polar trees PMID  
POWER 2005 web server Pipeline for phylogeny PMID  pdf
primetv 2007 UX, cygwin exe C++  Command line + simple GUI PMID   pdf
RadCon 2002 Mac RadCon  
SARAgene           
SeaView 2010 all C C++ PMID
ScripTree 2010 all Tcl Tk submitted
SpaceTree 2003 all Java (or Java Web Start)  
Spectronet 2002 Windows C++  
Spectrum 1997 Mac Windows Spectrum  
SplitsTree 2008 all Java. Trees and networks PMID   pdf
STE 2008 all Interactively exploring sets of phylogenetic trees. Java PMID    pdf
STEM 2009 ? species tree estimation using maximum likelihood for gene trees under coalescence. (C langage) PMID  
T-Rex 2005 web simplistic, also available for download  
TaxonTree 2003   TaxonTree  
THEA 2004 all Java. For DNA chip data analyses  
TREEBOLIC   all hyperbolic, Java  +web  
TreeAnalyzer 2004 all see MAST PMID
TREECON 1994 Windows TREECON  
Tree Draw Deck 1998 Mac OS9 HyperCard  
TreeDyn 2007   all Tcl/Tk   Online PMID pdf
TreeEdit 2002 MAC OSX TreEdit  
TreeExplorer 1999   for MEGA; outdated  
TREEFINDER 2005 all Java pdf
TreeGraph 2005 all C++, commande line  
TreeGraph2 2010 all Combining and visualizing evidence from different phylogenetic analyses. JAVA PMID   html
TreeIllustrator 2005 all Java (webstart or source) PMID  
TreeJuxtaposer 2004 all Java  
TreeMap 2004 all Java  
TreeMe 2005 Windows TreeMe   
TreePlus 2006 ???? Download ???, graph to tree ? pdf    ask for it
TreeQ-VISTA 2007 all functional annotations in phylogenetic context pdf
TreeSetViz 2004 Mac, Windows included in Mesquite  
TreeSimplifier 2006 Simplify trees using HUGO gene names PMID   pdf
TreeThief ???? Mac Scan images.  
TreeTool 1995 X windows  TreeTool  
TreeTracker 2007 perl detecting overrepresented clusters in a hierarchical tree PMID   pdf
TreeView (TV) 2001 all simple, goof copy/paste  
TreeView X 2005 all simple, less than 500 leaves manual
TreeWiz   applet 2002 all Java  
T-REX 2005 all phylogeny software  
UGENE 2010 all complete environment (similar to MEGA) manual
Walrus
 2005 all Hyperbolic 3D (Java) PMID  pdf  image

XML

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Graphs

Short descriptions.

3DPE. 3D Phylogeny Explorer (3DPE), a novel phylogeny tree viewer that maps trees onto three spatial axes (species on the X-axis; paralogs on Z; evolutionary distance on Y), enabling one to distinguish at a glance evolutionary features such as speciation; gene duplication and paralog evolution; lateral gene transfer; and violation of the "molecular clock" assumption. Users can input any tree on the online 3DPE, then rotate, scroll, rescale, and explore it interactively as "live" 3D views. All objects in 3DPE are clickable to display subtrees, connectivity path highlighting, sequence alignments, and gene summary views, and etc. To illustrate the value of this visualization approach for microbial genomes, we also generated 3D phylogeny analyses for all clusters from the public COG database. We constructed tree views using well-established methods and graph algorithms. We used Scientific Python to generate VRML2 3D views viewable in any web browser. CONCLUSION: 3DPE provides a novel phylogenetic tree projection method into 3D space and its web-based implementation with live 3D features for reconstruction of phylogenetic trees of COG database.
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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.
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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
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Archeopteryx the successor to ATV is a Java application based on the forester libaries for the visualization of annotated phylogenetic trees. It can be used both as applets (ArchaeopteryxA, ArchaeopteryxE) and as a standalone application.
Comments: I tried briefly. Seems quite complete, but I did not find the complete documentation. In the similar tools see ETE, TreeDyn and ScripTree. Each has similar features, but each would be more appropriate depending on what you are doing.
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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).
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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.
Bio::Phylo is a software library written in Perl 5, compatible with BioPerl. It provides a toolkit for the manipulation of rich phylogenetic data objects. The objects can be annotated and labeled, and have any number of arbitrary other objects attached to them. The objects can be traversed in various ways, including depth-first, breadth-first or level-order traversal of tree shapes and through iterator or visitor access.
Comments: Bio::Phylo most closely resembles the ape toolkit for R and the DendroPy toolkit for Python
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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.
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Bosque. Bosque is a distributed software environment oriented to manage the computational resources involved in typical phylogenetic analyses. Bosque has been implemented as a client-server application where the server  can execute installed phylogenetic programs (such as those present in the Phylip package, for example) and the client manages the results on a local relational database, although it can also execute phylogenetic programs locally, useful when no server is available. The client also performs the graphical visualisation and edition of trees and alignments, providing an environment for the analyses, from the integration of sequences to the printing of a final tree. One important feature of Bosque is that it allows multiple users to interact through the server, by talking on public channels and by sharing phylogenetic resources, such as sequences, trees, alignments, etc. This converts Bosque in one of the few peer-to-peer systems oriented to scientific collaboration. New 2008: Mac OSX version.
Comments: good evolution of the suite
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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.
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COMPONENT. COMPONENT is a computer program for analysing evolutionary trees and is intended for use in studies of phylogeny, tree shape distribution, gene trees/species trees, host-parasite cospeciation, and biogeography.
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CTree. CTree has been designed for the quantification of clusters within viral phylogenetic tree topologies. Clusters are stored as individual data structures from which statistical data, such as the Subtype Diversity Ratio (SDR), Subtype Diversity Variance (SDV) and pairwise distances can be extracted. This simplifies the quantification of tree topologies in relation to inter- and intra-cluster diversity. Here the novel features incorporated within CTree, including the implementation of a heuristic algorithm for identifying clusters, are outlined along with the more usual features found within general tree viewing software.
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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.
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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).
DendroPy. DendroPy is a cross-platform library for the Python programming language that provides for object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an emphasis on phylogenetic tree operations. DendroPy uses a splits-hash mapping to perform rapid calculations of tree distances, similarities and shape under various metrics. It contains rich simulation routines to generate trees under a number of different phylogenetic and coalescent models. DendroPy's data simulation and manipulation facilities, in conjunction with its support of a broad range of phylogenetic data formats (NEXUS, Newick, PHYLIP, FASTA, NeXML, etc.), allow it to serve a useful role in various phyloinformatics and phylogeographic pipelines. Availability: The stable release of the library is available for download and automated installation through the Python Package Index site (http://pypi.python.org/pypi/DendroPy), while the active development source code repository is available to the public from GitHub (http://github.com/jeetsukumaran/DendroPy).
Comments: Not tried yet
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Dendroscope. Researchers studying phylogenetic relationships need software that is able to visualize trees efficiently, increasingly of large datasets involving hundreds of thousands of taxa. The program should be user friendly (easy to run on all popular operating systems), facilitate interactive browsing and editing the trees and allow one to export the result in multiple file formats in publication quality.
Comments: to manipulate and visualize hudge trees.
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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.
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Drawtree. Drawtree is a program for visualisation of trees. It reads in trees in the Newick format and outputs them in a graphic format. Currently the only supported output format is Encapsulated PostScript, but other formats are planned.
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ETE ETE is a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. Besides a broad set of tree handling options, it provides specific methods to analyze phylogenetic and clustering trees. It supports large tree data structures, node annotation, independent editing and analysis of tree partitions, and the association of trees with external data such as multiple sequence alignments or numerical matrices. Finally, ETE implements a programmable tree drawing engine that can be used to automatize the graphical rendering of trees  with customized node-specific visualizations.
Comments: I tried it, I will use it as soon I have enough time to play with it. I am even thinking contributing functions :-).
ExploreTree was a winning entry in the Processing Time code jam. It takes descriptions of trees in Newick format and renders them in a zooming interface. It's written using the nifty visualization language Processing. ExploreTree is free software which you can distribute under the GNU GPLv2 or (at your option) any later version. You can download the source at github: exploretree, libnewicktree. The Newick parsing code in libnewicktree comes from the TreeJuxtaposer project, which is available under the BSD license.
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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.
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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 !
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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...
GenomeDiagram.  GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems.
Comments: Does not really belong to this list, but who knows...
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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.
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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.
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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.
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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.  
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iTOL. Interactive Tree Of Life (iTOL) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. Trees can be interactively pruned and re-rooted. Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported.
Jstree is  a web application as well as a Javascript library for parsing, manipulating and plotting phylogenetic trees in the Newick format. With Jstree, one can highlight subtrees or leaves, collapse nodes in viewing, swap children, reroot, delete clades, move nodes, and export tree images, all via mouse clicks. It is purely implemented in Javascript and HTML5, and is efficient enough for trees with hundreds leaves (half a second for a tree with 864 leaves), although this is web browser dependent. Jstree is the first Javascript based editor for phylogenetic trees.
Comments : It is web browser dependent rather than OS dependent. It is known to work with IE 8 (though slow), Opera, Firefox, Chrome and Safari. Compared to Scriptree (that runs on the server), Jstree  works purely on the client side (the tree is rendered by the local web browser). Thus jstree can be more responsive when the server is very busy, but Jstree has (yet) far less tree  operations possible and cannot be automated. Only one problem detected : the menu allowing to select operation done by clics disappeas when browsing down a large tree, it is then necessary to move up and down the tree to change the operation you want to apply to a node.
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K Tree Score. A new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees. To do this, the algorithm first scales one of the trees to have a global divergence as similar as possible to the other tree. Then, the branch length distance, which takes differences in topology and branch lengths into account, is applied to the two trees. We thus obtain the minimum branch length distance or K tree score. Two trees with very different relative branch lengths get a high K score whereas two trees that follow a similar among-lineage rate variation get a low score, regardless of the overall rates in both trees. There are several applications of the K tree score, two of which are explained here in more detail. First, this score allows the evaluation of the performance of phylogenetic algorithms, not only with respect to their topological accuracy, but also with respect to the reproduction of a given branch length variation. In a second example, we show how the K score allows the selection of orthologous genes by choosing those that better follow the overall shape of a given reference tree.
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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.
Madeline 2.0.  The Madeline 2.0 Pedigree Drawing Engine (PDE) is a pedigree drawing program for use in linkage and family-based association studies. The program is designed to handle large and complex pedigrees with an emphasis on readability and aesthetics. For complex pedigrees, we use a hybrid algorithm in which consanguinous loops are drawn as cyclic graphs whenever possible, but we resort to acyclic graphs when matings can no longer be connected without line crossings. A similar hybrid approach is used to avoid line crossings for matings between distant descendants of different founding groups. Written in object-oriented C++ and released under the GNU General Public License (GPL), Madeline 2.0 PDE reads input files specified on the command line and generates pedigree drawings without user interaction. Pedigree output in scalable vector graphics (SVG) format can be viewed in browsers with native SVG rendering support or in vector graphics editors. We provide an easy-to-use public web service, which is experimental and still under development. Availability: http://kellogg.umich.edu/madeline.
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MAST. Phylogenetic trees are used to represent the evolutionary history of a set of species. Comparison of multiple phylogenetic trees can help researchers find the common classification of a tree group, compare tree construction inferences or obtain distances between trees. We present TreeAnalyzer, a freely available package for phylogenetic tree comparison. A MAST (Maximum Agreement Subtree) algorithm is implemented to compare the trees. Additional features of this software include tree comparison, visualization, manipulation, labeling, and printing.
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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.
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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.
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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).
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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)
Comments: probably should not be in this list
NAViGaTOR.  NAViGaTOR is a powerful graphing application for the 2D and 3D visualization of biological networks. NAViGaTOR includes a rich suite of visual mark-up tools for manual and automated annotation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs. Publication-quality images can be rendered through SVG graphics export. NAViGaTOR supports community-developed data formats (PSI-XML, BioPax and GML), is platform-independent and is extensible through a plug-in architecture. AVAILABILITY: NAViGaTOR is freely available to the research community from http://ophid.utoronto.ca/navigator/. Installers and documentation are provided for 32- and 64-bit Windows, Mac, Linux and Unix.
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Nexplorer. Nexplorer is a web-based program for interactive browsing and manipulation of character data in NEXUS format, well suited for use with alignments and trees representing families of homologous genes or proteins. Users may upload a sequence family dataset, or choose from one of several thousand already available. Nexplorer provides a flexible means to develop customized views that combine a tree and a data matrix or alignment, to create subsets of data, and to output data files or publication-quality graphics.
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Newicktree. newicktree is a PSTricks-based LATEX package which enables phylogenetic trees described in the Newick format to be drawn directly into LATEX documents. mswordtree is a macro for producing phylogenetic trees using the drawing elements available in Microsoft Word.
Newick Utilities. A suite of UNIX shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes.
Comments: basic functions, no editing, no annotation.  See ScriptTree as a more powerfull alternative, but which requires to be installed
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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. But very effective, and copy/paste from NJplot to PowerPoint or Presentation produces a tree that can be ungrouped and easily modified.
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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.
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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.
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Panta rhei. The first version of the graphical multiple sequence alignment environment QAlign was published in 2003. Panta rhei extends QAlign by several features. Major redesigns on the user interface, for instance, allow users to flexibily compose views for multiple projects. The new sequence viewer handles datasets with arbitrarily many and arbitrarily large sequences that may still be edited by guided block moving. More distance-based algorithms are available to interactively reconstruct phylogenetic trees which can now also be zoomed and navigated graphicaly.
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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
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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.
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PHY.FI. The need to depict a phylogeny, or some other kind of abstract tree, is very frequently experienced by researchers from a broad range of biological and computational disciplines. Thousands of papers and talks include phylogeny figures, and often during everyday work, one would like to quickly get a graphical display of, e.g., the phylogenetic relationship between a set of sequences as calculated by an alignment program such as ClustalW or the phylogenetic package Phylip. A wealth of software tools capable of tree drawing exists; most are comprehensive packages that also perform various types of analysis, and hence they are available only for download and installing. Some online tools exist, too. RESULTS: This paper presents an online tool, PHY.FI, which encompasses all the qualities of existing online programs and adds functionality to hopefully eliminate the need for post-processing the phylogeny figure in some other general-purpose graphics program. PHY.FI is versatile, easy-to-use and fast, and supports comprehensive graphical control, several download image formats, and the possibility of dynamically collapsing groups of nodes into named subtrees (e.g. "Primates"). The user can create a color figure from any phylogeny, or other kind of tree, represented in the widely used parenthesized Newick format. CONCLUSION: PHY.FI is fast and easy to use, yet still offers full color control, tree manipulation, and several image formats. It does not require any downloading and installing, and thus any internet user regardless of computer skills, and computer platform, can benefit from it. PHY.FI
Comments: very simplistic, cannot at all compare to the best tools.
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Phylo_comparison. We describe an algorithm and 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 the phylogenies interactively, and clearly highlights those parts of the trees that differ, both in terms of topology and branch length.  The software is implemented as a Java applet. It is also available on request from the authors.
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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).
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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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PhyloGena. Phylogenomic approaches towards functional and evolutionary annotation of unknown sequences have been suggested to be superior to those based only on pairwise local alignments. User-friendly software tools making the advantages of phylogenetic annotation available for the ever widening range of bioinformatically uninitiated biologists involved in genome/EST annotation projects are, however, not available. We were particularly confronted with this issue in the annotation of sequences from different groups of complex algae originating from secondary endosymbioses, where the identification of the phylogenetic origin of genes is often more problematic than in taxa well represented in the databases (e.g. animals, plants or fungi). RESULTS: We present a flexible pipeline with a user-friendly, interactive graphical user interface running on desktop computers that automatically performs a basic local alignment search tool (BLAST) search of query sequences, selects a representative subset of them, then creates a multiple alignment from the selected sequences, and finally computes a phylogenetic tree. The pipeline, named PhyloGena, uses public domain software for all standard bioinformatics tasks (similarity search, multiple alignment, and phylogenetic reconstruction). As the major technological innovation, selection of a meaningful subset of BLAST hits was implemented using logic programming, mimicing the selection procedure (BLAST tables, multiple alignments and phylogenetic trees) are displayed graphically, allowing the user to interact with the pipeline and deduce the function and phylogenetic origin of the query. PhyloGena thus makes phylogenomic annotation available also for those biologists without access to large computing facilities and with little informatics background. Although phylogenetic annotation is particularly useful when working with composite genomes (e.g. from complex algae), PhyloGena can be helpful in expressed sequence tag and genome annotation also in other organisms.
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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.
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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. 
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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...
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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...
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PhyloView. PhyloView, a web based tool for colouring phylogenetic trees upon arbitrary taxonomic properties of the species represented in a protein sequence phylogenetic tree. Provided that the tree contains SwissProt, SpTrembl, or GenBank protein identifiers, the tool retrieves the taxonomic information from the corresponding database. A colour picker displays a summary of the findings and allows the user to associate colours to the leaves of the tree according to any number of taxonomic partitions. Then, the colours are propagated to the branches of the tree.
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PhyloWidget is PhyloWidget is a program for viewing, editing, and publishing phylogenetic trees online. It is small, contains a simple yet powerful user interface, and contains many novel features not available in other phylogenetic viewers. PhyloWidget is specifically designed for:
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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.
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Phyutility. Phyutility provides a set of phyloinformatics tools for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. Its simple command-line interface allows for easy integration into scripted analyses, and is able to handle large datasets with an integrated database.
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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 !).
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POWER. the PhylOgenetic WEb Repeater, is a web-based service designed to perform user-friendly pipeline phylogenetic analysis. POWER uses an open-source LAMP structure and infers genetic distances and phylogenetic relationships using well-established algorithms (ClustalW and PHYLIP). POWER incorporates a novel tree builder based on the GD library to generate a high-quality tree topology according to the calculated result. POWER accepts either raw sequences in FASTA format or user-uploaded alignment output files. Through a user-friendly web interface, users can sketch a tree effortlessly in multiple steps. After a tree has been generated, users can freely set and modify parameters, select tree building algorithms, refine sequence alignments or edit the tree topology. All the information related to input sequences and the processing history is logged and downloadable for the user's reference. Furthermore, iterative tree construction can be performed by adding sequences to, or removing them from, a previously submitted job.
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primetv. Evolutionary processes, such as gene family evolution or parasite-host co-speciation, can often be viewed as a tree evolving inside another tree. Relating two given trees under such a constraint is known as reconciling them. Adequate software tools for generating illustrations of tree reconciliations are instrumental for presenting and communicating results and ideas regarding these phenomena. Available visualization tools have been limited to illustrations of the most parsimonious reconciliation. However, there exists a plethora of biologically relevant non-parsimonious reconciliations. Illustrations of these general reconciliations may not be achieved without manual editing. RESULTS: We have developed a new reconciliation viewer, primetv. It is a simple and compact visualization program that is the first automatic tool for illustrating general tree reconciliations. It reads reconciled trees in an extended Newick format and outputs them as tree-within-tree illustrations in a range of graphic formats. Output attributes, such as colors and layout, can easily be adjusted by the user. To enhance the construction of input to primetv, two helper programs, readReconciliation and reconcile, accompany primetv. Detailed examples of all programs' usage are provided in the text. For the casual user a web-service provides a simple user interface to all programs. CONCLUSION: With primetv, the first visualization tool for general reconciliations, illustrations of trees-within-trees are easy to produce. Because it clarifies and accentuates an underlying structure in a reconciled tree, e.g., the impact of a species tree on a gene-family phylogeny, it will enhance scientific presentations as well as pedagogic illustrations in an educational setting. 
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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.
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ScripTree.  There is a large amount of tools for interactive display of phylogenetic trees. However, there is a shortage of tools for the automation of tree rendering. Scripting phylogenetic graphics would enable the saving of graphical analyses involving numerous and complex tree handling operations and would allow the automation of repetitive tasks. ScripTree is a tool intended to fill this gap. It is an interpreter to be used in batch mode. Phylogenetic graphics instructions are stored in a text file and performed in a sequential way. Such instructions are related to tree rendering as well as tree annotation. ScriptTree is written in Tcl/Tk making it a cross-platform application, e.g. suitable for Windows and Unix-like systems, including OS X. It can be used either as a standalone package or included in a bioinformatic pipeline and linked to a HTTP server. See the "Examples" section for a ScripTree demonstration by using a web interface. See the "Download & Install" section for downloading ScripTree and its user's manual
Comments: Not intended for biologist. Best use is included within a pipeline or a web server to automaticaly display complex trees on the fly. Much extended annotations facilities. I use it on one of my web sites
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SeaView.  SeaView version 4, is a multiplatform program designed to facilitate multiple alignment and phylogenetic tree building from molecular sequence data through the use of a graphical user interface. SeaView version 4 combines all the functions of the widely used programs SeaView (in its previous versions) and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees. In relation to the wide present offer of tools and algorithms for phylogenetic analyses, SeaView is especially useful for teaching and for occasional users of such software. SeaView is freely available.
Comments: I use it much, it is improving every year. The Linux interface is not as good and easy than the windows interface. Dont know about the Mac, but Manolo who wrote it is working on a Mac. Much appreciated : from the tree display windows, it is possible to reorder the sequences in the viewer the way they are on the tree.
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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.
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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.
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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.
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SplitsTree. SplitsTree provides a framework for the calculation of phylogenetic trees and networks. It contains a wide variety of methods for the import/export, calculation and visualization of phylogenetic information. The software is developed in Java and implements a command line tool as well as a graphical user interface. RESULTS: In this article, we present solutions to two important problems in the field of phylogenetic networks. The first problem is the visualization of explicit phylogenetic networks. To solve this, we present a modified version of the equal angle algorithm that naturally integrates reticulations into the layout process and thus leads to an appealing visualization of these networks. The second problem is the availability of explicit phylogenetic network methods for the general user. To advance the usage of explicit phylogenetic networks by biologists further, we present an extension to the SplitsTree framework that integrates these networks. By addressing these two problems, SplitsTree is among the first programs that incorporates implicit and explicit network methods together with standard phylogenetic tree methods in a graphical user interface environment. CONCLUSION: In this article, we presented an extension of SplitsTree 4 that incorporates explicit phylogenetic networks. The extension provides a set of core classes to handle explicit phylogenetic networks and a visualization of these networks.
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STE. A Java application for interactively exploring sets of phylogenetic trees using two coupled representations: a node-and-link diagram and a textual list of common clades. Selection, pruning, filtering or re-rooting in one representation is immediately reflected in the other. While summary trees are more effective at showing the relationship among clades, they can only show a consistent subset of those that appear in the textual list. Working with both representations mitigates the disadvantages of having to choose just one.
STEM.  STEM is a software package written in the C language to obtain maximum likelihood (ML) estimates for phylogenetic species trees given a sample of gene trees under the coalescent model. It includes options to compute the ML species tree, search the space of all species trees for the k trees of highest likelihood and compute ML branch lengths for a user-input species tree. AVAILABILITY: The STEM package, including source code, is freely available at http://www.stat.osu.edu/~lkubatko/software/STEM/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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T-Rex. Newick Viewer allows the user to visualize a tree coded by its newick string. Hierarchical, Axial and Radial types of tree drawing are available. Download or web site. Simplistic.
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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.
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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.
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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.
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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).
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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...).
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Tree Draw Deck. A Hypercard stack which draws phylogenetic trees. It is derived from Drawgram and Drawtree
Comments: deprecated.
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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.
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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.
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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 !
TreeGraph2. Today it is common to apply multiple potentially conflicting data sources to a given phylogenetic problem. At the same time, several different inference techniques are routinely employed instead of relying on just one. In view of both trends it is becoming increasingly important to be able to efficiently compare different sets of statistical values supporting (or conflicting with) the nodes of a given tree topology, and merging this into a meaningful representation. A tree editor supporting this should also allow for flexible editing operations and be able to produce ready-to-publish figures. RESULTS: We developed TreeGraph 2, a GUI-based graphical editor for phylogenetic trees (available from http://treegraph.bioinfweb.info). It allows automatically combining information from different phylogenetic analyses of a given dataset (or from different subsets of the dataset), and helps to identify and graphically present incongruences. The program features versatile editing and formatting options, such as automatically setting line widths or colors according to the value of any of the unlimited number of variables that can be assigned to each node or branch. These node/branch data can be imported from spread sheets or other trees, be calculated from each other by specified mathematical expressions, filtered, copied from and to other internal variables, be kept invisible or set visible and then be freely formatted (individually or across the whole tree). Beyond typical editing operations such as tree rerooting and ladderizing or moving and collapsing of nodes, whole clades can be copied from other files and be inserted (along with all node/branch data and legends), but can also be manually added and, thus, whole trees can quickly be manually constructed de novo. TreeGraph 2 outputs various graphic formats such as SVG, PDF, or PNG, useful for tree figures in both publications and presentations. CONCLUSION: TreeGraph 2 is a user-friendly, fully documented application to produce ready-to-publish trees. It can display any number of annotations in several ways, and permits easily importing and combining them. Additionally, a great number of editing- and formatting-operations is available.
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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).
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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.
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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 ?
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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).
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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.
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TreeQ-Vista. For presenting functional annotations in a phylogenetic context. Traits, such as phenotypic and genomic properties, are interactively queried from a user-provided relational database with a user-friendly interface which provides a set of tools for users with or without SQL knowledge. The query results are projected onto a phylogenetic tree and can be displayed in multiple color groups. A rich set of browsing, grouping and query tools are provided to facilitate trait exploration, comparison and analysis.
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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.
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TreeSimplifier.  Based on species tree information and HUGO gene names, it summarizes "monophyla". These monophyla correspond to subtrees of the gene tree where the evolution of a gene follows species phylogeny, and they are simplified to single leaves in the gene tree. Such a simplification may fail, for example, due to genes in the gene tree that are misplaced. In this way, misplaced genes can be identified. Optionally, our tool glosses over a limited degree of "paraphyly" in a further simplification step. In both simplification steps, species can be summarized into groups and treated as equivalent. In the present study we used our tool to derive a simplified tree of 397 leaves from a tree of 1138 leaves. Comparing the simplified tree to a "cartoon tree" created manually, we note that both agree to a high degree. CONCLUSION: Our automatic simplification tool for gene trees is fast, accurate, and effective. It yields results of similar quality as manual simplification. It should be valuable in phylogenetic studies of large protein families.
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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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TreeTracker. a novel strategy to compare a hierarchical and a dichotomic non-hierarchical classification of elements, in order to find clusters in a hierarchical tree in which elements of a given "flat" partition are overrepresented. The key improvement of our strategy respect to previous methods is using permutation analyses of ranked clusters to determine whether regions of the dendrograms present a significant enrichment. We show that this method is more sensitive than previously developed strategies and how it can be applied to several real cases, including microarray and interactome data. Particularly, we use it to compare a hierarchical representation of the yeast mitochondrial interactome and a catalogue of known mitochondrial protein complexes, demonstrating a high level of congruence between those two classifications. We also discuss extensions of this method to other cases which are conceptually related.
 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. Native graphics file format (PICT on Macintosh, Windows metafile on Windows) for copying pictures into other applications, and for saving graphics files. The program currently reads trees with up to to 1000 taxa.
Comments: limited to trees with less than 1000 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.
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TreeView X. TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It has a subset of the functionality of the version of TreeView available for the Mac Classic and Windows (it is roughly equivalent to version 0.95 of TreeView).
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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.
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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.
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UGENE UGENE is a free cross-platform genome analysis suite. It works  on Windows, Mac OS or Linux and requires only a few clicks to install. Unipro UGENE is a free visual software solution for DNA and protein sequence analysis. The functionality of UGENE can be significantly extended with plugins. Check plugins documentation to learn more about plugins after reading the manual. It includes a sequence viewer, aligners, annotations editor and a phylogenetic tree viewer. Comments: not tested yet, in the same category see also MEGA and SEAVIEW.
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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.
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Some repositories

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Richard Christen.    July  2010