MELANIE VIEWER 7.0.7 – Visualize Gels and Related Data obtained from Melanie

MELANIE VIEWER 7.0.7

:: DESCRIPTION

Melanie Viewer is made available free of charge to help researchers visualize gels and related data obtained through the use of the full version of Melanie by colleagues. It can also be used to view annotated gels from databases such as SWISS-2DPAGE, or any other image files with an appropriate format (.tif, .gel, …).

::DEVELOPER

The Proteome Informatics group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MELANIE VIEWER

:: MORE INFORMATION

NAViGaTOR 3.0 – Visualize and Analyze Protein-protein Interaction Networks.

NAViGaTOR 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

GsmPlot – Web Server to visualize Epigenome data in NCBI

GsmPlot

:: DESCRIPTION

GsmPlot is a web service to automatically download, analyze and visualize epigenetics data (ChIP-Seq, ATAC-Seq, Bis-Seq), public from NCBI or private from you.

::DEVELOPER

Deqiang Sun Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics, 21 (1), 55 2020 Feb 12
GsmPlot: A Web Server to Visualize Epigenome Data in NCBI
Jia Li , Yue Yin , Mutian Zhang , Jie Cui , Zhenhai Zhang , Zhiyong Zhang , Deqiang Sun

Reputer – Compute and Visualize Repeat Structures

Reputer

:: DESCRIPTION

The REPuter program family provides state of the art software solutions to compute and visualize repeats in whole genomes or chromosomes.

::DEVELOPER

Prof. Dr. Stefan Kurtz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX/ Linux

:: DOWNLOAD

 Reputer

:: MORE INFORMATION

Citation

S. Kurtz, J. V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, R. Giegerich:
REPuter: The Manifold Applications of Repeat Analysis on a Genomic Scale.
Nucleic Acids Res., 29(22):4633-4642, 2001.

KGML-ED 1.0 – Edit, Process, and Visualize KGML pathway files

KGML-ED 1.0

:: DESCRIPTION

KGML-ED supports the dynamic exploration and editing of KEGG Pathway diagrams. It is a graphical network editor, that provides read- and write-support for the KGML (KEGG Markup Language) file format. Pathway files are loaded and transformed into a graph network which may be modified to fulfill user-specific needs (e.g. it is possible, to delete or add network elements, change labels and colors). Novel network exploration approaches are supported by the system as well.

::DEVELOPER

KGML-ED team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • Java

:: DOWNLOAD

 KGML-ED

:: MORE INFORMATION

Citation

Christian Klukas and Falk Schreiber
Dynamic exploration and editing of KEGG pathway diagrams.
Bioinformatics 2007 23: 344-350.

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