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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

ArkMAP

ArkMAP is a desktop application to draw and align genetic and genomic maps, retrieved from remote data sources or loaded as local files. Maps can be retrieved from our public map database ArkDB or from any Ensembl data source (i.e. Ensembl and Ensembl Genomes). By using the JEnsembl API, maps can be drawn for any release version of any of the thousands of species present in Ensembl data sources, allowing not only inter-specific comparisons, but also comparisons between different versions/revisions of assembled genomes. Maps can be aligned by relating identical or synonymous markers across maps, or through the gene homology/orthology relationship data stored in the Ensembl Compara databases, allowing ready visualization of regions of conserved synteny between species. The map drawing canvas is highly configurable, supports interactive exploration of maps, markers and relationships and allows export of publication quality graphics.

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Institution: University of Edinburgh

GenotypeChecker

GenotypeChecker is a desktop software tool for assisting data cleansing. The application identifies likely data errors in pedigree/genotype data sets by performing an inheritance-checking algorithm for each marker across the pedigree, and highlights inconsistently inherited genotypes in an exploratory user interface. By ‘masking’ suspect datapoints and rechecking inheritance consistency, erroneous datapoints can be confirmed and cleansed from the data set. The software, examples and documentation are freely available at http://bioinformatics.roslin.ac.uk/genotypechecker.

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Institution: The University of Edinburgh

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

PhyloDet

    PhyloDet is a scalable tree visualization that enables biologists to visualize multiple traits or attributes mapped to large evolutionary trees with thousands of leaf nodes representing the species. It also preserves branch lengths that indicate the genetic similarity between two species. PhyloDet is interactive, enabling users to set any node of the tree as the root and to show or hide any branches without re-layout of the tree. PhyloDet enables biologists to visualize complex interactions and how they relate to the evolutionary history of the species.
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Institution: Yonsei University, Seoul, Korea

Strudel

Strudel is a graphical tool for visualizing genetic and physical maps of genomes for comparative purposes. The application aims to let the user examine their data at a variety of different levels of resolution, from entire maps to individual markers, and explore syntenic relationships between genomes. All browsing and interaction with Strudel happens in real-time – there is no need to wait while the maps are generated.

Strudel is built using Java 1.6 and ships with its own JRE, so there is no need for users to install or update Java.

Features:

  • Visualize multiple genomes and thousands of homologies interactively and in real time
  • Continuous zoom ranging from entire genome views to singles features
  • Explore intervals such as QTLs and list annotation for features
  • Search for features by name
  • Filter homologies on display by BLAST e-value
  • Single genome mode also supported
  • Ships with example dataset to facilitate familiarization with the software
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Institution: The James Hutton Institute, Dundee University

HerbariaViz

HerbariaViz is a web mapping application that provides space–time–species data query responses efficiently. The open-source methods for aggregating point data spatially and temporally, outline our approach to sound cartographic representations of those data, and detail the design of a client interface for making requests and mapping responses. A focus group session involving domain experts was performed to provide user evaluation of the application. In our discussion, we present potential avenues of future work, including: facilitating query response comparisons, handling incomplete and inaccurate data, and generalizing the method presented.

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Institution: GeoVISTA Center, Penn State University

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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Jalview

Jalview is a free program for protein and nucleic acid multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. The Jalview Desktop can also connect with databases and analysis services, and provides a graphical interface to the alignment and analysis services provided by the JavA Bioinformatics Analysis Web Services framework.  From Jalview 2.8.2, the Jalview desktop also interfaces with the Chimera molecular visualisation system to provide powerful 3D graphics tightly coupled to Jalview's functions.

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Institution: University of Dundee

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