and Tree - softwares for visualisation and manipulations
Dealing with phylogenetic trees - a "comprehensive list"
Also some additional utiliies
See by category the "best
software: send a mail christen(replace)unice.fr
Submit a review, changes, suggestions, send mail to adress above
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
of available tools. updated 2010/07. Most recent in red
clic for a short description
||MS Windows. OSX
||Python + VRML2.
Some 3D capabilities.
|| Linux Mac
|| complete environnement
||requires Sun Java
(now replaced by Archaeopteryx)
||compare 2 trees
comparisons, reconciled trees
||analysis of clusters
within trees (Java)
||Display manipulate hudge trees. Java
||included in PHYLIP.
||Used by the
phylogenetic tree of life
not really a tree viewer
||web hyperbolic tree
|K tree score
||Compare 2 trees. Perl
||all (source code)
||a new program for
local and web-based pedigree drawing (C++)
||???. In fact published as
(uses Tree Set Viz).
||requires .NET Framework 1.1
||Network Analysis, Visualization and Graphing Toronto
||Latex: draw newick
in Latex documents or Word
||Very simple, but
powerfull and copy/paste to vector format
||same as NJplot
application. Java applet
web, see also web app
moduleinteractively exploring sets of phylogenetic trees
standalone: assembly of the tree-of-trees database
||Taxonomic coloring of
server or download source code
||fast and easy online creation and manipulation of
phylogeny color figures.
and manipulating phylogenetic trees
||Pipeline for phylogeny
||UX, cygwin exe
Command line + simple GUI
||Java (or Java Web
||Java. Trees and
||Interactively exploring sets of phylogenetic trees. Java
||species tree estimation
using maximum likelihood for gene trees under coalescence. (C
available for download
||Java. For DNA chip data analyses
||for MEGA; outdated
||C++, commande line
visualizing evidence from different phylogenetic analyses. JAVA
||Download ???, graph to
||pdf ask for it
||functional annotations in phylogenetic context
using HUGO gene names
overrepresented clusters in a hierarchical tree
||simple, goof copy/paste
||simple, less than
(similar to MEGA)
||Hyperbolic 3D (Java)
||PMID pdf image
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.
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
Reference manual pdf
APE is mostly an environment to develop and
new analytical methods. It has little capacities for tree manipulations
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.
Visualisation only. Requires an immersive display platform
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
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.
(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
allows an extended newick format, uses it to find orthologous sequences
and gene duplications (using a second species tree).
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
Can save trees as images.
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.
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
Comments: Bio::Phylo most closely resembles the ape toolkit for R and the DendroPy toolkit for Python
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.
Commercial, not tried. Looks like an integrated tool for the molecular
biologist, with no extended capacities for tree manipulation and
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.
good evolution of the suite
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.
applet available from authors.
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.
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.
DAMBE.Xia, X., and
2001 DAMBE: Data analysis in molecular biology and evolution. Journal
of Heredity 92:371-373.
for windows. This is an integrated software for molecular phylogeny
with basic capabilities for tree edition.
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.
for the Mac. Basic function, plus some editing, an interesting option:
change the proportion of two branches at the root.
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
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
Not tried yet
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.
to manipulate and visualize hudge trees.
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
historical, was probably the first "good" tree visualisation program.
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.
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
I tried it, I will use it as soon I have enough time to play with it. I
am even thinking contributing functions :-).
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
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,
The Newick parsing code in libnewicktree comes from the TreeJuxtaposer
project, which is available under the BSD license.
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.
refers to ATV above.
Geneious puts core
bioinformatics functions within the reach of all
molecular biologists and biochemists in an application that is as easy
to use as email.
Geneious does sequence alignment, 3D structure visualization,
phylogenetic tree building, sequence analysis, publication-search and
more; all in a single application.
A commercial program for free !
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.
for comparisons of two trees, a species tree and a gene tree and find
about duplications, orthologs...
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.
Does not really belong to this list, but who knows...
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.
initially developed for visualization of graphs derived from a web
site. Visualisation only.
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.
online and download, visualize and move a tree in hyperbolic context.
No annotation, no edition.
HYPERTREE is a
tree viewer, with a hyperbolic ('fish-eye') view and editing abilities
that help in managing very large trees.
visualize and move a tree in hyperbolic context. No annotation, no
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.
The goal of the HyperTree Java Library is to provide a library to ease
the implementation of hyperbolic tree visualization. See also Treemaps.
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.
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
(half a second for a tree with 864 leaves), although this is web browser dependent.
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.
Tree Score. A new phylogenetic comparison method that
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.
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.
commercial. Parsimony oriented,Edit sequences, change tree topology.
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:
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.
Mavric is a python
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.
basic functions, edit labels, prune & graft.
MEGA is an
integrated tool for
automatic and manual sequence alignment, inferring phylogenetic trees,
mining web-based databases, estimating rates of molecular
evolution, and testing evolutionary hypotheses.
Phylogeny, sequences oriented, a complete software for aligning
sequences, phylogeney and making trees, with some capabilities for tree
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.
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).
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
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),
enhanced metafile (EMF), bitmap (BMP), or Portable network graphics
tried yet -.NET requirement)
probably should not be in this list
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.
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.
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.
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
basic functions, no editing, no annotation. See ScriptTree as
more powerfull alternative, but which requires to be installed
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.
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.
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
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.
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.
rhei. The first version of the graphical multiple sequence
environment QAlign was published in 2003. Panta rhei extends QAlign by
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
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.
commercial. Not tried
phpPhylotree is a
web application that is able to draw phylogenetic trees.
it produces an SVG (Scalable Vector Graphic) file from phylip/newick
no comment yet.
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
very simplistic, cannot at all compare to the best tools.
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.
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
dating from 1999, this is probably now outdated (basic functions, some
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.,
also seems to date back from 2000, this
is probably now outdated (basic functions, some editing).
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.
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
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.
a perl script to draw a tree in its simplest format.
Phylogenetic Tree Viewer.
Visualize the progression of a single DNAml computation over time by
stacking up 2D trees (time samples) in the third dimension.
current version uses the third dimension for easy comparison of any
number of tree files.
visualisation only, the "planes" visualisation is an interesting
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
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
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
an interesting approach for people who do not know how to make trees.
Could be easily ported to other phylogenies...
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.
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:
- Visually exploring small, medium and large phylogenetic
- Editing trees with a simple, intuitive user interface
- Creating publication-quality tree figures
- Interfacing with databases through a URL-based API
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.
environment for building trees. Basic options for visualization of
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.
(Polar and Interactive Tree) is an application that allows to build,
visualize and customize phylogenetic trees in a polar interactive and
highly flexible view.
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 !).
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
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.
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.
no comment yet.
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.
Commercial product, not tried.
There is a large amount of tools for interactive
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
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
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.
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.
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
described as designed to deal with large trees. I was not able to open
a tree with the Java Web Start app.
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.
Non tree-like data visualisation.
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.
little capability for tree editing, was not written for that.
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
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
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
INFORMATION: Supplementary data are available at Bioinformatics online.
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.
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.
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
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.
No edition, but powerfull tree annotation tool using ontologies.
Treebolic is an
applet whose purpose is to give a hyperbolic rendering of hierarchical
takes a tree in XML format. No annotation no manipulation.
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.
Takes sequences and make a tree using various methods. Basic function
for tree representation, allows some edition (fonts, colors, colapse,
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.
includes some editing tools (collapse, taxon edition...).
Tree Draw Deck. A
Hypercard stack which draws phylogenetic trees. It is derived from
Drawgram and Drawtree
TreeDyn is a full
featured environment for drawing trees, manipulation and annotation.
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.
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.
takes aligned sequences and compute a ml tree (seems efficient) with
plenty of options; only basic tools for tree representation.
TreeGraph assists in
producing complex ready-to-publish figures of phylogenetic trees. The
TGF format used by the program automates formatting of several
different statistical support value types (confidence estimates) per
tree node. Moreover, internal text and graphical labels are
automatically arranged at the nodes as are annotations for clades or
groups of terminals. TREEGRAPH imports NEXUS trees and related file
formats. Beyond common tree edit operations, simultaneous pruning of
subtrees (simplification of the tree to higher order clades) and saving
of subtrees is possible. TREEGRAPH exports to the standard vector
graphics formats Scalable Vector Graphics and PostScript.
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 !
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.
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.
commercial, part of The SeqPad software suite, not tried.
Compare phylogenetic evolutionary trees interactively and
automatically. Uses nested parentheses (Newick/New Hampshire) data
format. Guaranteed visibility of marked regions provides visual
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.
a tool to compare two trees and find similarities/differences. Minimal
documentation and non intuitive software (webstart tried).
Treemap is a
space-constrained visualization of hierarchical
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
unconventional ! Clearly a different manner to represent trees. No
editing or manipulation tools. Makes use of annotation files that
contain labels assigned to each leaf of the tree. Color code the "tree"
according to these annotations. Finally it is also possible to use some
kind of hybrid representation that mix the "tremap" structure with a
conventional tree near the root. The tree is displayed mid-rooted.
TreeMe is a
phylogenetic tree visualization and manipulation software for
phylogenetics and research in evolution.
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 ?
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)
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).
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.
no download page, no documentation.
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.
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.
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.
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.
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...
developed by RDP (and maintained by) TreeTool includes all basic
operations as well as collpase, prune, coloring and some basic editing
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.
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.
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.
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).
is mostly a phylogeny software with some drawing capacities.
some very interesting implentation of phylogenetic algorithms. In
particular makes use of reticulation and can plot it. Very basic tree
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
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.
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
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
Interesting for visualisation of very very large datasets.
Visualisation and navigation only.
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