List of phylogenetic tree visualization software

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OneZoom OneZoom Hominidae.png
OneZoom

This list of phylogenetic tree viewing software is a compilation of software tools and web portals used in visualizing phylogenetic trees.

Contents

Online software

NameDescriptionLicense
Annotations QUick Analysis for PhylOgeNY (Aquapony [1] )Javascript tree viewer for Beast CeCILL
ETE toolkit Tree Viewer [2] an online tool for phylogenetic tree view (newick format) that allows multiple sequence alignments to be shown together with the trees (fasta format)
EvolView [3] an online tool for visualizing, annotating and managing phylogenetic trees
IcyTree [4] Client-side Javascript SVG viewer for annotated rooted trees. Also supports phylogenetic networks
Iroki [5] Automatic customization and visualization of phylogenetic trees
iTOL - interactive Tree Of Life [6] annotate trees with various types of data and export to various graphical formats; scriptable through a batch interface
Microreact [7] Link, visualise and explore sequence and meta-data using phylogenetic trees, maps and timelines
OneZoom [8] uses IFIG (Interactive Fractal Inspired Graphs) to display phylogenetic trees which can be zoomed in on to increase detail
Lifemap [9] Fractal-like representation to provide an interactive explorer of the tree of life "à la google maps"
Phylo.io [10] View and compare up to 2 trees side by side with interactive HTML5 visualisations
PhyloExplorer [11] a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database.
PHYLOViZ Online [12] Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees
PhyloWidget [13] view, edit, and publish phylogenetic trees online; interfaces with databases
PRESTO [14] a Phylogenetic tReE viSualisaTion.
Taxonium [15] web-based tool for exploration of very large trees including those with millions of nodes, with search and metadata coloring. When provided with a mutation-annotated tree, it illustrates mutations on the tree and displays final genotypes.
T-REX (Webserver) [16] Tree inference and visualization (hierarchical, radial and axial tree views), Horizontal gene transfer detection and HGT network visualization
TidyTree [17] A client-side HTML5/SVG Phylogenetic Tree Renderer, based on D3.js
TreeVector [18] scalable, interactive, phylogenetic trees for the web, produces dynamic SVG or PNG output, implemented in Java

Desktop software

NameDescriptionOS1Citation
ARBAn integrated software environment for tree visualisation and annotationLM [19]
Archaeopteryx Java tree viewer and editor (used to be ATV) [20]
BioNumerics Universal platform for the management, storage and analysis of all types of biological data, including tree and network inference of sequence dataW [21]
Dendroscope An interactive viewer for large phylogenetic trees and networksAll [22]
DensiTreeA viewer capable of viewing multiple overlaid trees.All [23]
FigTree Simple Java tree viewer able to read newick and nexus tree files. Can be used to color branches and produce vector artwork.All [24]
JEvTraceA multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace [25] and other phylogeny-inspired analysis.All [26]
MEGA Software for statistical analysis of molecular evolution. It includes different tree visualization featuresAll [27]
MultiDendrogramsInteractive open-source application to calculate and plot phylogenetic treesAll [28]
PHYLOViZPhylogenetic inference and data visualization for allelic/SNP sequences profiles using Minimum Spanning TreesAll [29]
SplitsTree Software for viewing trees, cladograms, NeighborNets, and other graphsAll [30]
TreeDynOpen-source software for tree manipulation and annotation allowing incorporation of meta informationAll [31]
TreevolutionOpen-source tool for circular visualization with section and ring distortion and several other features such as branch clustering and pruningAll [32]
TreeGraph 2Open-source tree editor with numerous editing and formatting operations including combining different phylogenetic analysesAll [33]
TreeViewTreeviewing softwareAll [34] [35]
UGENE An opensource visual interface for Phylip 3.6 packageAll [36]
TreeViewer Flexible, modular software to visualise and manipulate phylogenetic treesAll [37]

1 "All" refers to Microsoft Windows, Apple OSX and Linux; L=Linux, M=Apple Mac, W=Microsoft Windows

Libraries

NameLanguageDescriptionCitation
Bio.PhyloPython Phylo: Part of Biopython, this module provides classes, functions and I/O support for working with phylogenetic trees [38]
Bio::PhyloPerlA collection of Perl modules for manipulating and visualizing phylogenetic data. Bio::Phylo is one part of a comprehensive suite of Perl biology tools [21]
CGRphylo RPipeline based on CGR method for accurate classification and tracking of rapidly evolving viruses [39]
ETE PythonETE (Environment for Tree Exploration) is a toolkit that assists in the automated manipulation, analysis and visualization of trees. [40]
ggtree RAn R package for tree visualization and annotation with grammar of graphics supported [41]
GraPhlAn Python GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees.
jsPhyloSVGJavascriptopen-source javascript library for rendering highly-extensible, customizable phylogenetic trees; used for Elsevier's interactive trees [42] [43]
PhyD3Javascriptinteractive phylogenetic tree visualization with numerical annotation graphs, with SVG or PNG output, implemented in D3.js [44]
phylotree.jsJavascriptphylotree.js is a library that extends the popular data visualization framework D3.js, and is suitable for building JavaScript applications where users can view and interact with phylogenetic trees [45]
PhyloPlots.jlJulia PhyloPlots.jl is a julia package for plotting phylogenetic trees and networks, integrated with PhyloNetworks.jl [46]
PhytoolsRPhylogenetic Tools for Comparative Biology (and Other Things) based in R [47]
toytree PythonToytree: A minimalist tree visualization and manipulation library for Python [48]

See also

Related Research Articles

<span class="mw-page-title-main">Sequence homology</span> Shared ancestry between DNA, RNA or protein sequences

Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal gene transfer event (xenologs).

<span class="mw-page-title-main">Conserved sequence</span> Similar DNA, RNA or protein sequences within genomes or among species

In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids or proteins across species, or within a genome, or between donor and receptor taxa. Conservation indicates that a sequence has been maintained by natural selection.

A phylogenetic network is any graph used to visualize evolutionary relationships between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes instead of only tree nodes. Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree, the R-package, phangorn, and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.

In mathematics and phylogenetics, Newick tree format is a way of representing graph-theoretical trees with edge lengths using parentheses and commas. It was adopted by James Archie, William H. E. Day, Joseph Felsenstein, Wayne Maddison, Christopher Meacham, F. James Rohlf, and David Swofford, at two meetings in 1986, the second of which was at Newick's restaurant in Dover, New Hampshire, US. The adopted format is a generalization of the format developed by Meacham in 1984 for the first tree-drawing programs in Felsenstein's PHYLIP package.

<span class="mw-page-title-main">Roderic D. M. Page</span> New Zealand-born evolutionary biologist

Roderic Dugald Morton Page is a New Zealand-born evolutionary biologist at the University of Glasgow, Scotland, and the author of several books. As of 2015 he is professor at the University of Glasgow and was editor of the journal Systematic Biology until the end of 2007. His main interests are in phylogenetics, evolutionary biology and bioinformatics.

The Database of Macromolecular Motions is a bioinformatics database and software-as-a-service tool that attempts to categorize macromolecular motions, sometimes also known as conformational change. It was originally developed by Mark B. Gerstein, Werner Krebs, and Nat Echols in the Molecular Biophysics & Biochemistry Department at Yale University.

<span class="mw-page-title-main">UTOPIA (bioinformatics tools)</span>

UTOPIA is a suite of free tools for visualising and analysing bioinformatics data. Based on an ontology-driven data model, it contains applications for viewing and aligning protein sequences, rendering complex molecular structures in 3D, and for finding and using resources such as web services and data objects. There are two major components, the protein analysis suite and UTOPIA documents.

Anders Krogh is a bioinformatician at the University of Copenhagen, where he leads the university's bioinformatics center. He is known for his pioneering work on the use of hidden Markov models in bioinformatics, and is co-author of a widely used textbook in bioinformatics. In addition, he also co-authored one of the early textbooks on neural networks. His current research interests include promoter analysis, non-coding RNA, gene prediction and protein structure prediction.

Archaeopteryx is an interactive computer software program, written in Java, for viewing, editing, and analyzing phylogenetic trees. This type of program can be used for a variety of analyses of molecular data sets, but is particularly designed for phylogenomics. Besides tree description formats with limited expressiveness, it also implements the phyloXML format. Archaeopteryx is the successor to Java program A Tree Viewer (ATV).

SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP. Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.

Computational Resources for Drug Discovery (CRDD) is an important module of the in silico module of Open Source for Drug Discovery (OSDD). The CRDD web portal provides computer resources related to drug discovery, predicting inhibitors, and predicting the ADME-Tox properties of molecules on a single platform. It caters to researchers researching computer-aided drug design by providing computational resources, and hosting a discussion forum. One of the major objectives of CRDD is to promote open source software in the field of cheminformatics and pharmacoinformatics.

A supertree is a single phylogenetic tree assembled from a combination of smaller phylogenetic trees, which may have been assembled using different datasets or a different selection of taxa. Supertree algorithms can highlight areas where additional data would most usefully resolve any ambiguities. The input trees of a supertree should behave as samples from the larger tree.

PhylomeDB is a public biological database for complete catalogs of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions which are based on the analysis of the phylogenetic trees. The automated pipeline used to reconstruct trees aims at providing a high-quality phylogenetic analysis of different genomes, including Maximum Likelihood tree inference, alignment trimming and evolutionary model testing.

Horizontal or lateral gene transfer is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate investigations of the evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages.

Arndt von Haeseler is a German bioinformatician and evolutionary biologist. He is the scientific director of the Max F. Perutz Laboratories at the Vienna Biocenter and a professor of bioinformatics at the University of Vienna and the Medical University of Vienna.

<span class="mw-page-title-main">Phylogenetic reconciliation</span> Technique in evolutionary study

In phylogenetics, reconciliation is an approach to connect the history of two or more coevolving biological entities. The general idea of reconciliation is that a phylogenetic tree representing the evolution of an entity can be drawn within another phylogenetic tree representing an encompassing entity to reveal their interdependence and the evolutionary events that have marked their shared history. The development of reconciliation approaches started in the 1980s, mainly to depict the coevolution of a gene and a genome, and of a host and a symbiont, which can be mutualist, commensalist or parasitic. It has also been used for example to detect horizontal gene transfer, or understand the dynamics of genome evolution.

References

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