Dendroscope 3.6.3 – Visualize Phylogenetic Trees & Rooted Networks

Dendroscope 3.6.3

:: DESCRIPTION

Dendroscope is a software for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

Dendroscope

:: MORE INFORMATION

Citation:

Daniel H Huson, Daniel C Richter, Christian Rausch, Tobias Dezulian, Markus Franz and Regula Rupp.
Dendroscope: An interactive viewer for large phylogenetic trees,
BMC Bioinformatics. 2007 Nov 22;8(1):460

Circoletto 20160709 – Visualize Sequence Similarity with Circos

Circoletto 20160709

:: DESCRIPTION

Circoletto is a rather beautiful way to visualise sequence similarity from BLAST results (which you can either create through Circoletto, or upload your own).

::DEVELOPER

The Bioinformatics Analysis Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • BLAST
  • Circos

:: DOWNLOAD

 Circoletto

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Oct 15;26(20):2620-1. Epub 2010 Aug 24.
Circoletto: visualizing sequence similarity with Circos.
Darzentas N.

Haploscope – Visualize Haplotype Diversity

Haploscope

:: DESCRIPTION

Haploscope is a software package that facilitates flexible rendering of images to aid interpretation of model-based summaries of population haplotypes. Haploscope is designed to accept haplotype frequency input directly from output files of fastPHASE (Scheet & Stephens, 2006), though output from other cluster-based models for population haplotypes could be adapted for input to Haploscope.

::DEVELOPER

paul scheet lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Haploscope

:: MORE INFORMATION

Citation

San Lucas, F. A., Rosenberg, N. A. and Scheet, P. (2012),
Haploscope: a tool for the graphical display of haplotype structure in populations.
Genetic Epidemiology, 36: 17-21. doi: 10.1002/gepi.20640.

Circos 0.69-2 – Visualize Genome Data and Information in Circular Layout

Circos 0.69-2

:: DESCRIPTION

Circos is a software package for visualizing genome data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.

::DEVELOPER

Martin Krzywinski | Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

 

:: REQUIREMENTS

  • Windows / Linux /
  • Perl

:: DOWNLOAD

 Circos

:: MORE INFORMATION

Citation

Krzywinski, M. et al.
Circos: an Information Aesthetic for Comparative Genomics.
Genome Res (2009) 19:1639-1645

Marvin 16.5.2.0 – Draw & Visualize Chemistry

Marvin 16.5.2.0

:: DESCRIPTION

Marvin is a collection of tools for drawing, displaying and characterizing chemical structures, substructures and reactions.

::DEVELOPER

ChemAxon Ltd.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Marvin

:: MORE INFORMATION

GenomeStudio 20151207 – Visualize and Analyze data generated by all of Illumina’s platform

GenomeStudio 20151207

:: DESCRIPTION

GenomeStudio is a software to visualize and analyze data generated by all of Illumina’s platform.This powerful informatics solution supports the primary analysis of sequence-based data produced by the Genome AnalyzerIIx and microarray-based data generated by the iScan System. Performance optimized tools and a user-friendly graphical interface allow you to quickly and easily convert data into meaningful results for your genome analysis and research.

::DEVELOPER

Illumina

:: SCREENSHOTS

GenomeStudio

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GenomeStudio

:: MORE INFORMATION

Citation

Methods Mol Biol. 2011;784:77-98. doi: 10.1007/978-1-61779-289-2_6.
Gene expression profiling in formalin-fixed, paraffin-embedded tissues using the whole-genome DASL assay.
April CS, Fan JB.

FISH Oracle 2 – Visualize Data from multiple Array CGH or SNP Array Experiments

FISH Oracle 2

:: DESCRIPTION

FISH Oracle is a web-based software to visualize data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and  zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats (PDF, PS, PNG, SVG).

::DEVELOPER

RESEARCH GROUP FOR GENOME INFORMATICS ,Center for Bioinformatics, University of Hamburg

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX
  • MySQL
  • Java
  • Apache Tomcat server
  • GenomeTools

:: DOWNLOAD

  FISH Oracle

:: MORE INFORMATION

Citation

M. Mader, R. Simon, S. Steinbiss and S. Kurtz:
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
Journal of Clinical Bioinformatics, 1:20 (2011)

clusterMaker2 0.9.5 – Creat and Visualize Cytoscape Clusters

clusterMaker2 0.9.5

:: DESCRIPTION

UCSF clusterMaker is a Cytoscape plugin that unifies different clustering techniques and displays into a single interface. Current clustering algorithms include hierarchical, k-medoid, AutoSOME, and k-means for clustering expression or genetic data; and MCL, transitivity clustering, affinity propagation, MCODE, community clustering (GLAY), SCPS, and AutoSOME for partitioning networks based on similarity or distance values. Hierarchical, k-medoid, AutoSOME, and k-means clusters may be displayed as hierarchical groups of nodes or as heat maps. All of the network partitioning cluster algorithms create collapsible “meta nodes” to allow interactive exploration of the putative family associations within the Cytoscape network, and results may also be shown as a separate network containing only the intra-cluster edges, or with inter-cluster edges added back

::DEVELOPER

the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UCSF

:: SCREENSHOTS

clusterMaker

:: REQUIREMENTS

:: DOWNLOAD

 clusterMaker

:: MORE INFORMATION

Citation:

clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE.
BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436.

LCR-eXXXplorer – Search, Visualize and Share data for low Complexity Regions in Protein sequence

LCR-eXXXplorer

:: DESCRIPTION

LCR-eXXXplorer is a web-service designed to assist biologists in displaying, searching and sharing Low Complexity Regions (LCRs) contained within protein sequences.

::DEVELOPER

LCR-eXXXplorer team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences.
Kirmitzoglou I, Promponas VJ.
Bioinformatics. 2015 Feb 20. pii: btv115.

NAViGaTOR 2.3.0 – Visualize and Analyze Protein-protein Interaction Networks.

NAViGaTOR 2.3.0

:: DESCRIPTION

NAViGaTOR (Network Analysis, Visualization, & Graphing TORonto ) is a software package for visualizing and analyzing protein-protein interaction networks.NAViGaTOR can query OPHID / I2D – online databases of interaction data – and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI).

::DEVELOPER

Jurisica Lab of the Ontario Cancer Institute

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 NAViGaTOR

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Dec 15;25(24):3327-9. doi: 10.1093/bioinformatics/btp595. Epub 2009 Oct 16.
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto.
Brown KR1, Otasek D, Ali M, McGuffin MJ, Xie W, Devani B, Toch IL, Jurisica I.

Djebbari, A., Ali, M., Otasek, D., Kotlyar. M., Fortney, K., Wong, S., Hrvojic, A. and Jurisica, I.
NAViGaTOR: Scalable and Interactive Navigation and Analysis of Large Graphs.
Internet Mathematics, 7(4):314-347, 2011