Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses…
Desktop app
Tree Building guided… Tree Building guided by Species Tree

TreeBest Tree Building guided by Species Tree

Builds, manipulates and displays phylogenetic trees. TreeBest is particularly…

Builds, manipulates and displays phylogenetic trees. TreeBest is particularly designed for building gene trees with a known species tree and is highly efficient and accurate. It is previously known…

Desktop app
MullerPlot MullerPlot

MullerPlot

Generates Muller plot from parental, genealogy, phylogeny information and…

Generates Muller plot from parental, genealogy, phylogeny information and population, abundance, frequency dynamics data. Muller plots combine information about succession of different OTUs…

Desktop app
Newick Utilities Newick Utilities

Newick Utilities

A suite of UNIX shell programs for processing any number of phylogenetic trees…

A suite of UNIX shell programs for processing any number of phylogenetic trees of any size. Newick Utilities performs frequently-used tree operations without requiring user interaction. It allows…

Desktop app
TreeScaper TreeScaper

TreeScaper

An application for tree set visualization as well as the identification of…

An application for tree set visualization as well as the identification of distinct phylogenetic signals. TreeScaper allows users to accomplish many different tasks, including (i) computing pairwise…

Web app
MetaTreeMap MetaTreeMap

MetaTreeMap

A JavaScript module that implements a set of modules for visual analysis of…

A JavaScript module that implements a set of modules for visual analysis of metagenomic data. MetaTreeMap allows to visualize phylogenic trees in a compact manner that focuses on rendering the…

Desktop app
Dissimilarity… Dissimilarity Analysis and Representation

DARwin Dissimilarity Analysis and Representation

A package for diversity and phylogenetic analysis on the basis of evolutionary…

A package for diversity and phylogenetic analysis on the basis of evolutionary dissimilarities. DARwin is mainly focused on diversity structure description based on distance methods, organized in…

Web app
Graphical… Graphical Phylogenetic Analysis

GraPhlAn Graphical Phylogenetic Analysis

A tool for compact and publication-quality representation of circular taxonomic…

A tool for compact and publication-quality representation of circular taxonomic and phylogenetic trees with potentially rich sets of associated metadata. GraPhlAn was developed primarily for…

Desktop app
DensiTree DensiTree

DensiTree

Provides a quick method for qualitative analysis of tree sets. The main idea…

Provides a quick method for qualitative analysis of tree sets. The main idea behind DensiTree is to draw all trees in the set transparently. As a result, areas where a lot of the trees agree in…

Web app
Treelink Treelink

Treelink

A platform-independent software for linking datasets and sequence files to…

A platform-independent software for linking datasets and sequence files to phylogenetic trees. Treelink allows an automated integration of datasets to trees for operations such as classifying a tree…

Desktop app
DendroPy DendroPy

DendroPy

A cross-platform library for the Python programming language that provides…

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…

Web app
EvolView EvolView

EvolView

A comprehensive web application for visualizing, annotating and managing…

A comprehensive web application for visualizing, annotating and managing phylogenetic trees. Evolview allows users to visualize phylogenetic trees in various formats, customize the trees through…

Desktop app
Archaeopteryx Archaeopteryx

Archaeopteryx

A software tool for the visualization, analysis, and editing of potentially…

A software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. Archaeopteryx is entirely written in the Java programming language. It can…

Web app
Tree-Based Alignment… Tree-Based Alignment Selector

T-BAS Tree-Based Alignment Selector

Visualizes phylogenetic relationships and metadata for Pezizomycotina,…

Visualizes phylogenetic relationships and metadata for Pezizomycotina, downloads alignments for six loci and performs placement of unknowns using either BLAST or phylogeny-based approaches in RAxML.…

Web app
Desktop app
drawStrees drawStrees

drawStrees

Allows interactive drawing of generalized suffix tree. drawStrees takes one or…

Allows interactive drawing of generalized suffix tree. drawStrees takes one or more short sequences as input and returns the corresponding suffix tree.

Web app
Desktop app
Coalator Coalator

Coalator

An interactive program for drawing coalescent trees.

An interactive program for drawing coalescent trees.

Desktop app
Java based… Java based Phylogenetic Tree Viewer

JTreeView Java based Phylogenetic Tree Viewer

A basic tree viewer that lets you view, reroot, rotate nodes and edit further…

A basic tree viewer that lets you view, reroot, rotate nodes and edit further aspects of New Hampshire bracket format trees.

Desktop app
ColorPhylo ColorPhylo

ColorPhylo

An automatic colour coding scheme to visualise the levels of taxonomic…

An automatic colour coding scheme to visualise the levels of taxonomic relationships displayed as overlay on any kind of data plot. ColorPhylo creates a method linking a given knowledge on a dataset…

Web app
Desktop app
PHYLOViZ PHYLOViZ

PHYLOViZ

A user-friendly software that allows the combined analysis of multiple data…

A user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. PHYLOViZ Online was developed to allow users to do these…

Desktop app
ALVIS ALVIS

ALVIS

An open-source platform for the joint explorative analysis of multiple sequence…

An open-source platform for the joint explorative analysis of multiple sequence alignments and phylogenetic trees, employing Sequence Bundles as its main visualization method. Alvis combines the…

Web app
Phylo.io Phylo.io

Phylo.io

A web application to visualise and compare phylogenetic trees side-by-side. Its…

A web application to visualise and compare phylogenetic trees side-by-side. Its distinctive features are: highlighting of similarities and differences between two trees, automatic identification of…

Web app
TreeVersity TreeVersity

TreeVersity

A web based interactive data visualization tool that allows users to analyze…

A web based interactive data visualization tool that allows users to analyze change in datasets by creating dynamic hierarchies based on the data attributes. TreeVersity2 introduces a novel space…

Web app
Desktop app
Wasabi Wasabi

Wasabi

An open source, web-based environment for evolutionary sequence analysis.…

An open source, web-based environment for evolutionary sequence analysis. Wasabi visualizes sequence data together with a phylogenetic tree within a modern, user-friendly interface: The interface…

Desktop app
Web app
G T A T C G C T A Visual Omics Explorer Visual Omics Explorer

VOE Visual Omics Explorer

A cross-platform data visualization portal that is implemented using only HTML…

A cross-platform data visualization portal that is implemented using only HTML and JavaScript code. VOE is a standalone software that can be loaded offline on the web browser from a local copy of the…

Desktop app
tree editor tree editor

tred tree editor

A tool to visualize and edit phylogenetic trees. tred combines a browser-based…

A tool to visualize and edit phylogenetic trees. tred combines a browser-based Javascript client with a Python (web2py) server. Trees are rendered in SVG using Raphael.This tool is simple,…

Desktop app
dendextend dendextend

dendextend

An R package for creating and comparing visually appealing tree diagrams.…

An R package for creating and comparing visually appealing tree diagrams. dendextend provides utility functions for manipulating dendrogram objects (their color, shape, and content) as well as…

Desktop app
CompareTrees5 CompareTrees5

CompareTrees5

Compares trees with each other and measures their similarity in topology and…

Compares trees with each other and measures their similarity in topology and branch lengths. Typically it is used to compare a known "true" tree with one or more estimated trees in order to…

Desktop app
YBYRÁ YBYRÁ

YBYRÁ

Integrates software solutions for data analysis in phylogenetics. It comprises…

Integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis…

Desktop app
BioJS DAGViewer BioJS DAGViewer

BioJS DAGViewer

A reusable JavaScript component made available as part of the BioJS project and…

A reusable JavaScript component made available as part of the BioJS project and intended to be used to display graphs of structured data, with a particular emphasis on Directed Acyclic Graphs (DAGs).…

Desktop app
RootAnnotator RootAnnotator

RootAnnotator

Allows for the easy determination of branch root posterior probability from any…

Allows for the easy determination of branch root posterior probability from any posterior sample of clocked trees. RootAnnotator makes use of posterior collections of trees generated under clock…

Desktop app
MASTtreedist MASTtreedist

MASTtreedist

A maximum agreement subtree (MAST)-based comparison metric in Mesquite's…

A maximum agreement subtree (MAST)-based comparison metric in Mesquite's Tree Set Viz module. This comparison module provides a new tree-tree pairwise comparison metric based on the differences…

Desktop app
PhyloGrapher PhyloGrapher

PhyloGrapher

A program designed to visualize and study evolutionary relationships within…

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…

Desktop app
Web app
Phylomatic Phylomatic

Phylomatic

An online phylogenetic query tool where users submit a list of taxa (e.g. from…

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…

Desktop app
SplitsTree SplitsTree

SplitsTree

An application for computing unrooted phylogenetic networks from molecular…

An application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, SplitsTree will compute a phylogenetic…

Desktop app
TreeJuxtaposer TreeJuxtaposer

TreeJuxtaposer

An application for browsing trees and comparing them side by side. Although it…

An application for browsing trees and comparing them side by side. Although it was originally designed to support phylogenetic trees, TreeJuxtaposer can be used on trees in any application domain.

Desktop app
Treevolution Treevolution

Treevolution

A tool for the representation and exploration of phylogenetic trees that…

A tool for the representation and exploration of phylogenetic trees that facilitates visual analysis. There are several useful tools to visualize phylogenetic trees, but their level of interaction is…

Desktop app
Walrus Walrus

Walrus

A tool for interactively visualizing large directed graphs in three-dimensional…

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,…

Desktop app
PhyloDraw PhyloDraw

PhyloDraw

A unified viewing tool for phylogenetic trees. PhyloDraw supports various kinds…

A unified viewing tool for phylogenetic trees. PhyloDraw supports various kinds of multi-alignment formats (Dialign2, Clustal-W, Phylip format, NEXUS, MEGA, and pairwise distance matrix) and…

Desktop app
PhyloGena PhyloGena

PhyloGena

A flexible pipeline with a user-friendly, interactive graphical user interface…

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…

Desktop app
Spectronet Spectronet

Spectronet

A package for the analysis and visualization of complex evolutionary data that…

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, Spectronet works by computing a…

Desktop app
Tree Set Visualization Tree Set Visualization

TreeSetViz Tree Set Visualization

Summarizes large sets of phylogenetic trees. TreeSetViz depicts a "tree…

Summarizes large sets of phylogenetic trees. TreeSetViz depicts a "tree space" using multi-dimensional scaling based on tree-to-tree distance metrics.

Desktop app
Treebolic Treebolic

Treebolic

A Java widget meant to provide a hyperbolic rendering of hierarchical data. The…

A Java widget meant to provide a hyperbolic rendering of hierarchical data. The Treebolic Generator is an application that allows the XML description to be generated. The Treebolic Browser is an…

Desktop app
MixtureTree annotator MixtureTree annotator

MixtureTree annotator

Allows the user to automatically color any phylogenetic tree in Newick format…

Allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically…

Desktop app
Ceiba Ceiba

Ceiba

A program for visualization and navigation of large phylogenetic trees, and…

A program for visualization and navigation of large phylogenetic trees, and annotation of these trees with collections of images. Ceiba is not a program for building phylogenies or analyzing…

Web app
CompPhy CompPhy

CompPhy

A web-based collaborative platform for comparing phylogenies. CompPhy offers…

A web-based collaborative platform for comparing phylogenies. CompPhy offers functionalities for tree edition, tree comparison, supertree inference and data management in a collaborative environment.…

Desktop app
ggtree ggtree

ggtree

A phylogenetic tree viewer for different types of tree annotations. ggtree…

A phylogenetic tree viewer for different types of tree annotations. ggtree extends the ggplot2 plotting system which implemented the grammar of graphics. It is designed for not only viewing…

Desktop app
Mesquite Mesquite

Mesquite

A modular, extendible software tool for evolutionary biology, designed to help…

A modular, extendible software tool for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of…

Desktop app
Web app
ScripTree ScripTree

ScripTree

A tool for scripting phylogenetic graphics. ScripTree allows the management of…

A tool for scripting phylogenetic graphics. ScripTree allows the management of multiple trees and usual kinds of annotations. It can be used either as a stand-alone package or included in a pipeline…

Desktop app
TopiaryExplorer TopiaryExplorer

TopiaryExplorer

Supports the visualization of very large phylogenetic trees, including features…

Supports the visualization of very large phylogenetic trees, including features such as the automated coloring of branches by environmental data, manipulation of trees and incorporation of per-tip…

Desktop app
Web app
OneZoom OneZoom

OneZoom

It is committed to heightening awareness about the diversity of life on earth,…

It is committed to heightening awareness about the diversity of life on earth, its evolutionary history and the threats of extinction. OneZoom allows you to explore the tree of life in a completely…

Web app
Phylogeny Javascript… Phylogeny Javascript Information Visualiser and…

PhyloJIVE Phylogeny Javascript Information Visualiser and Explorer

A web-based application that integrates biodiversity information aggregated…

A web-based application that integrates biodiversity information aggregated from many sources with phylogenetic trees. PhyloJIVE demonstrates that it is possible and useful to assemble interactive…

Desktop app
Web app
PhyTB PhyTB

PhyTB

A web-based tool to assist phylogenetic tree visualisation and identification…

A web-based tool to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism. Variant call format files can be uploaded to determine a sample…

Desktop app
Genetic Programming… Genetic Programming Tree Visualizer

Genetic Programming Tree Visualizer

Java classes that allow easy visualization of genetic programming (GP) trees.…

Java classes that allow easy visualization of genetic programming (GP) trees. With the help of these objects you can easily export graphic images representing your trees. You can see what a tree…

Desktop app
Web app
TaxonTree TaxonTree

TaxonTree

Combines dynamic query interfaces and zoomable graphics to visually accommodate…

Combines dynamic query interfaces and zoomable graphics to visually accommodate highly interconnected data such as the Linnaean hierarchy for kingdom Animalia. Because the structure of the data is…

Desktop app
TreeMe TreeMe

TreeMe

Visualization, editing and annotation of phylogenetic trees. Features:…

Visualization, editing and annotation of phylogenetic trees. Features: visualisation of large phylogenetic trees (>1000 OTUs); combine trees: unites bootstrap labels of several trees onto a single…

Desktop app
TreePlus TreePlus

TreePlus

An interactive graph visualization system based on a tree-style layout.…

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…

Desktop app
TreeTracker TreeTracker

TreeTracker

Detects overrepresented clusters in a hierarchical tree. TreeTracker compares a…

Detects overrepresented clusters in a hierarchical tree. TreeTracker compares a hierarchical and a dichotomic non-hierarchical classification of elements, in order to find clusters in a hierarchical…

Desktop app
Baobab Baobab

Baobab

A Java user interface dedicated to viewing and editing large phylogenetic…

A Java user interface dedicated to viewing and editing large phylogenetic trees. Original features include: (i) a colour-mediated overview of magnified subtrees; (ii) copy/cut/paste of (sub)trees…

Desktop app
CTree CTree

CTree

A program designed for the quantification of clusters within viral phylogenetic…

A program 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…

Desktop app
HyperTree HyperTree

HyperTree

An application to visualize and navigate large trees in hyperbolic space.…

An application to visualize and navigate large trees in hyperbolic space. HyperTree includes color-coding, search mechanisms and navigational aids, as well as focus+context viewing, allowing enormous…

Desktop app
NJplot NJplot

NJplot

A tree drawing program able to draw any phylogenetic tree expressed in the…

A tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format. NJplot is especially convenient for rooting the unrooted trees obtained from parsimony,…

Desktop app
TreeIllustrator TreeIllustrator

TreeIllustrator

A user-friendly application to visualize and customize phylogenetic trees.…

A user-friendly application to visualize and customize phylogenetic trees. TreeIllustrator has a broad range of functions and capabilities, such as dragging of nodes, different tree shapes, zooming…

Desktop app
TreeDyn TreeDyn

TreeDyn

A tool using annotations and dynamic graphical methods for editing and…

A tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window,…

Desktop app
BayesTrees BayesTrees

BayesTrees

A program designed to visually interact with samples of trees, in particular…

A program designed to visually interact with samples of trees, in particular Bayesian samples. BayesTrees reads files in nexus format.

Desktop app
Dendroscope Dendroscope

Dendroscope

A program for working with rooted phylogenetic trees and networks. Dendroscope…

A program for working with rooted phylogenetic trees and networks. Dendroscope provides a number of methods for drawing and comparing rooted phylogenetic networks, and for computing them from rooted…

Desktop app
Environment for Tree… Environment for Tree Exploration

ETE Environment for Tree Exploration

A python programming toolkit that assists in the automated manipulation,…

A python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as…

Desktop app
FigTree FigTree

FigTree

It is designed as a graphical viewer of phylogenetic trees and as a program for…

It is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. In particular FigTree is designed to display summarized and annotated trees…

Web app
PhyloWidget PhyloWidget

PhyloWidget

A program for viewing, editing, and publishing phylogenetic trees online.…

A program for viewing, editing, and publishing phylogenetic trees online. PhyloWidget is small, contains a simple yet powerful user interface, and contains many novel features not available in other…

Web app
Tree and reticulogram… Tree and reticulogram REConstruction

T-REX Tree and reticulogram REConstruction

A web server dedicated to the reconstruction of phylogenetic trees,…

A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events. T-REX includes several popular bioinformatics…

Desktop app
TreeViz TreeViz

TreeViz

A software tool for fast interactive visualization of large data structures…

A software tool for fast interactive visualization of large data structures organized in a tree. TreeViz allows quickly drilling down into points of interest in the data structure and rendering the…

Web app
interactive Tree Of… interactive Tree Of Life

iTOL interactive Tree Of Life

An online tool for the display and manipulation of phylogenetic trees. iTOL…

An online tool for the display and manipulation of phylogenetic trees. iTOL provides most of the features available in other tree viewers, and offers a novel circular tree layout, which makes it easy…

Desktop app
jsPhyloSVG jsPhyloSVG

jsPhyloSVG

An open-source javascript library specifically built for rendering…

An open-source javascript library specifically built for rendering highly-extensible, customizable phylogenetic trees. jsPhyloSVG can render complex trees, yet offers a simple method to do so. It…

Desktop app
Web app
Phylodendron Phylodendron

Phylodendron

A web application for drawing phylogenetic trees, used in evolutionary biology.…

A web application for drawing phylogenetic trees, used in evolutionary biology. Options allow you to save in various formats, print, edit, modify, and adorn the tree.

Web app
PhyloExplorer PhyloExplorer

PhyloExplorer

Facilitates assessment and management of phylogenetic tree collections. Given…

Facilitates assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the…

Desktop app
Web app
TreeVector TreeVector

TreeVector

A scalable vector graphics-and Java-based method that allows trees to be…

A scalable vector graphics-and Java-based method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required, and can be modified and linked…

Web app
Hypergeny Hypergeny

Hypergeny

An online tool for viewing large phylogenetic trees. Hypergeny helps…

An online tool for viewing large phylogenetic trees. Hypergeny helps researchers visualise and understand large phylogenetic trees by offering a hyperbolic tree browser.

Desktop app
MrEnt MrEnt

MrEnt

A program for drawing high-quality, printable phylogenetic trees. MrEnt…

A program for drawing high-quality, printable phylogenetic trees. MrEnt recognizes the standard Nexus tree format and the annotated tree files produced by BEAST and MrBayes. It combines in a single…

Desktop app
TreeGraph TreeGraph

TreeGraph

A graphical editor for phylogenetic trees which allows you to apply lots of…

A graphical editor for phylogenetic trees which allows you to apply lots of graphical formats to the elements of your tree. Moreover, TreeGraph supports several (visible or invisible) annotations…

Desktop app
TreeView Deprecated TreeView

TreeView

Provides a simple way to view the phylogenetic trees produced by a range of…

Provides a simple way to view the phylogenetic trees produced by a range of programs, such as PAUP*, PHYLIP, TREE-PUZZLE, and ClustalX. TreeView generates publication quality trees. The program can…

Desktop app
3D Phylogeny Explorer Deprecated 3D Phylogeny Explorer

3DPE 3D Phylogeny Explorer

A phylogeny tree viewer that maps trees onto three spatial axes (species on the…

A 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…

Desktop app
jPHYDIT Deprecated jPHYDIT

jPHYDIT

A Java application designed to furnish a visual and integrated environment for…

A Java application designed to furnish a visual and integrated environment for molecular phylogeny. jPHYDIT can be used to visualize intra-strand base-pairing information in secondary and tertiary…

Desktop app
newicktree Deprecated newicktree

newicktree

A PSTricks-based LATEX package which enables phylogenetic trees described in…

A PSTricks-based LATEX package which enables phylogenetic trees described in the Newick format to be drawn directly into LATEX documents. The syntax for including a phylogenetic tree in a document…

Desktop app
TreeSimplifier Deprecated TreeSimplifier

TreeSimplifier

A simplification tool for gene trees called TreeSimplifier. Based on species…

A simplification tool for gene trees called TreeSimplifier. Based on species tree information and HUGO gene names, it summarizes "monophyla". These monophyla correspond to subtrees of the…

Desktop app
Paloverde Paloverde

Paloverde

A program designed to help visualize the phylogenetic structure of moderately…

A program designed to help visualize the phylogenetic structure of moderately large trees--trees on the scale of 100-2500 leaf nodes. Paloverde embeds the user in an interactive virtual 3D world in…

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