Softwares for tree visualisation and manipulation
Richard Christen - firstname.lastname@example.org, April 2006
|Program web site||Update||OS||Comment & short description|
|ARB||2003||Linux Mac OSX||complete environnement|
|ATV||2002||all||Java(see also FORESTER°|
|Compare 2 trees||2006||applet||compare 2 trees|
|Drawtree and DrawGram...||1998||included in PHYLIP|
|FORESTER||2002||Java relies on ATV|
|Hypergeny||web hyperbolic tree browser|
|HyperTree Java||2001||HyperTree Java|
|Mesquite||2005||all||complete environment (uses Tree Set Viz).|
|MrEnt||2006||Windows||requires .NET Framework 1.1|
|NJplot unrooted||same as NJplot|
|Paloverde||2006||all||3D C OpenGL|
|Phylodendron||1999||all||Java + web|
|Phylogenetic Tree Drawing||2003||all||perl module|
|Phylogenetic Tree Viewer||2000||IRIX6.5||for dnaml|
|Phylomatic||2006||web, and standalone|
|Phylo_win||1996||all||environnement, uses njplot|
|SpaceTree||2003||all||Java (or Java Web Start)|
|TREEBOLIC||all||hyperbolic, Java +web|
|Tree Draw Deck||1998||Mac OS9||HyperCard|
|TreeExplorer||1999||for MEGA; outdated|
|TreeGraph||2005||all||C++, commande line|
|TreeIllustrator||2005||all||Java (webstart or source)|
|TreeSetViz||2004||Mac, Windows||included in Mesquite|
|Walrus||2005||all||Hyperbolic 3D (Java)|
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
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.
(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
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.
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.
Bosque (means forest
spanish) is a free graphical tool that allows easily
to draw, manipulate and prints phylogenetic trees in the newick format,
is the typical output format from phylogenetic programs, such as the
ones present on the Phylip package
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.
DAMBE.Xia, X., and
2001 DAMBE: Data analysis in molecular biology and evolution. Journal
of Heredity 92:371-373.
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).
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
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
FORESTER is being
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.
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.
GeneTree is a
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.
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.
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.
HYPERTREE is a
tree viewer, with a hyperbolic ('fish-eye') view and editing abilities
that help in managing very large trees.
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.
MacClade is a
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.
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.
Mesquite is software
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.
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
NJplot is a tree
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.
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
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.
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.
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.
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.,
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
Phylogenetic Tree Viewer.
Visualize the progression of a single DNAml computation over time by
stacking up 2D trees (time samples) in the third dimension.
current version uses the third dimension for easy comparison of any
number of tree files.
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.
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
a graphical colour interface for molecular phylogenetic inference.
It performs neighbor-joining, parsimony and maximum likelihood methods
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
for codon sequences. Species and sites to include in the analysis are
selected by mouse. Reconstructed trees can be drawn, edited, printed,
and evaluated according to numerous criteria.
(Polar and Interactive Tree) is an application that allows to build,
visualize and customize phylogenetic trees in a polar interactive and
highly flexible view.
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.
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
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.
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
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.
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. .
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
hierarchically organized biological datasets.
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.
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.
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.
TreeDyn is a full
featured environment for drawing trees, manipulation and annotation.
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.
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.
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.
Compare phylogenetic evolutionary trees interactively and
automatically. Uses nested parentheses (Newick/New Hampshire) data
format. Guaranteed visibility of marked regions provides visual
Treemap is a
space-constrained visualization of hierarchical
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
TreeMe is a
phylogenetic tree visualization and manipulation software for
phylogenetics and research in evolution.
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.
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.
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...
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.
is mostly a phylogeny software with some drawing capacities.
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
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
1. Bederson, B.B., B. Shneiderman, and M.
Wattenberg, Ordered and Quantum Treemaps: Making Effective Use of 2D
Space to Display Hierarchies. ACM Transactions on Graphics (TOG), 21,
(4), October 2002, 833-854. , 2002.