Phylogenetics

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OneZoom

OneZoom is an interactive map of the evolutionary relationships between the species on our planet. Trees with millions of tips, richly embellished with additional data, can now be easily explored within the web browser of any modern hardware with a zooming user interface similar to that used in Google Maps.

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Institution: OneZoom CIO & Imperial College London

Version 1 developed at Imperial College London. Version 2 and 3 developed at OneZoom CIO.

FigTree

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

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Institution: The University of Edinburgh

BioJS

BioJS is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies.

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Institution: BioJS

ViPhy

ViPhy supports comparison of multiple phylogenetic trees. It relies on a set of interactive views comparing phylogenetic trees on various detail levels. The views incorporate information on similarity scores and allow highlighting of similar structures in multiple trees. They thereby reveal global and local tree similarities.

 

Video: http://www.gris.tu-darmstadt.de/research/vissearch/projects/ViPhy/Intera...
Program Files: ViPhy.zip || Version 1.3.1 (16.02.2014)

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Institution: TU Darmstadt

Aequatus

We present the Aequatus, a web-based tool with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures among differing species or subtypes of a common species. The Aequatus utilises web technologies to provide a fast and intuitive browsing experience over complex comparative data. The Aequatus processes and visualises data directly from the Ensembl Compara and Ensembl Core schema databases by using precalculated genomic alignments from Ensembl Compara and relating them to Ensembl Core to gather genomic feature information, visualising phylogenetic and structural relationships among them via CIGAR strings. Whilst applicable to species with high-quality gold-standard reference genomes such as human or mouse, the Aequatus was designed with large fragmented genome references in mind,  e.g. polyploid plants. The ultimate goal of the Aequatus is to provide a unique and informative way to render and explore complex relationships between genes from various species.

Source Code: https://github.com/TGAC/Aequatus

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Institution: Earlham Institute

NN-tanglegram

Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multigene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks. Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NN-tanglegram method.
We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets. Availability: The algorithm is implemented in our program Dendroscope 3, which is freely available from www.dendroscope.org.

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Institution: Center for Bioinformatics (ZBIT), Tübingen University, Sand 14, 72076 Tübingen, Germany; ; Institut des Sciences de l’Evolution Montpellier (ISEM), CNRS UMR 5554, Université Montpellier II, Montpellier, France

TaxonTree

TaxonTree 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 visualized, the interface should be suitable both for biologists and for the general public. Names of organisms are essential to any biological database, including genomic databases, so a tool that allows effective searching and browsing of these names has wide application. 

TaxonTree allows full-text searching and browsing of a large, widely used multimedia database, University of Michigan's Animal Diversity Web via a classification of almost 200,000 animal names. At higher levels, binary branching illustrates relationships, and synapomorphies supporting those relationships are also available.  Scientific names have been compiled fromITIS, the UMMZ Bird Division, the EMBL Reptile DatabaseMammal Species of the World, and material from University of Maryland's BSCI 224 course taught by Jeff Jensen.

DoubleTree is an an application for comparing two trees using coupled interaction. DoubleTree is built on TaxonTree.

TaxonTree is built on SpaceTree, one of the HCIL Products.

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Institution: Cornell University

Dendroscope

The program is a visualization tool for large phylogenetic trees and rooted phylogenetic networks. Now on v3.

The program is open source and installers are available for Windows 10, MacOS X and Linux

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Institution: University of Tubingen

v.3 released.

Silva Tree Viewer

The SILVA Tree Viewer is a web application to browse and query the SILVA guide trees. 

The SILVA rRNA database project is a comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.

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Institution: Max Planck Institute for Marine Microbiology

ARB

The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and amino acid sequence data as well. A central database contains processed (aligned) primary structure data. Any additional descriptive data can be stored in database fields assigned to the individual sequences or linked via local or worldwide networks. A phylogenetic tree visualized in the main window can be used for data access and visualization. The package comprises additional tools for data import and export, sequence alignment, primary and secondary structure editing, profile and filter calculation, phylogenetic analyses, specific hybridization probe design and evaluation and other components for data analysis. Currently, the package is used by numerous working groups worldwide.

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