BiLayout 1.0 – Cytoscape plugin for Analysis & Visualization of Molecular Interaction Networks

BiLayout 1.0

:: DESCRIPTION

BiLayout is a Java plugin for Cytoscape, a software platform for the analysis and visualization of molecular interaction networks. This plugin computes a bipartite network layout for 2 user-selected groups of nodes.

::DEVELOPER

Max-Planck-Institut Informatik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BiLayout

:: MORE INFORMATION

SeqVis 1.5 – Visualization of Compositional Heterogeneity in Large Alignments of Nucleotides

SeqVis 1.5

:: DESCRIPTION

SeqVis is a stand-alone, platform-independent Java application developed with the aim to facilitate analysis and 3D visualization of compositional heterogeneity in species-rich alignments of nucleotide sequences. Each sequence is represented by a dot in a tetrahedron plot (i.e., an extension of the de Finetti), where the position of the dot depends uniquely on the nucleotide content of that sequence. Sequences that are compositionally different will appear as dots found in different areas within the tetrahedron. SeqVis also allows users to analyse their data set using, for example, the useful matched-pairs test of symmetry (Ababneh et al. 2006)

::DEVELOPER

Lars S. Jermiin

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOs / Linux / Unix
  • Java

:: DOWNLOAD

  SeqVis

:: MORE INFORMATION

Citation:

Ho JWK, Adams CE, Lew JB, Matthews TJ, Ng CC, Shahabi-Sirjani A, Tan LH, Zhao Y, Easteal S, Wilson SR, Jermiin LS (2006).
SeqVis: Visualization of compositional heterogeneity in large alignments of nucleotides.
Bioinformatics 22, 2162-2163.

NOC 3.01 – Molecular Explorer for Protein Structure Visualization

NOC 3.01

:: DESCRIPTION

NOC (also known as NOCH)  is a free molecular explorer for protein structure visualization, validation and analysis. It allows for import of molecular structures described in the Protein Data Bank file format.

::DEVELOPER

M.E. Chen, H.X. Cang, H. Nymeyer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

NOC

:: MORE INFORMATION

N/A

Biodesigner 0.75 – Molecular Modeling & Visualization

Biodesigner 0.75

:: DESCRIPTION

Biodesigner is a molecular modeling and visualization program for personal computers.Biodesigner is capable of creating homologous models of proteins, evaluate, and refine the models.

::DEVELOPER

Piotr Rotkiewicz

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Biodesigner

:: MORE INFORMATION

For further information please contact Piotr Rotkiewicz

 

Friend 2.0 – Multiple Structure Visualization & Multiple Sequence Alignment

Friend 2.0

:: DESCRIPTION

Friend (Integrated FRont-END) is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structure alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families.

::DEVELOPER

ilyin lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

Friend

:: MORE INFORMATION

Citation:

Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics. 2005 Sep 15(18):3677-8.

VisBio 3.40rc1 – Biological Visualization Tool

VisBio 3.40rc1

:: DESCRIPTION

VisBio is a biological visualization tool designed for easy visualization and analysis of multidimensional image data.VisBio provides 3D rendered views of multi-dimensional images that can be manipulated in 3D in real-time.

VisBio, using the remote OME Java API, can interact with OME directly for both reading and writing of image data.

::DEVELOPER

the Laboratory for Optical and Computational Instrumentation group

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

VisBio ; Source code

:: MORE INFORMATION

VisBio is an open source project.

VIZARD 1.2 – Affymetrix GeneChip® Data Analysis & Visualization

VIZARD 1.2

:: DESCRIPTION

VIZARD is a Java program for analysis and visualization of Affymetrix GeneChip® data.VIZARD includes several integrated tools for filtering, sorting, clustering and visualization of gene expression data as well as tools for discovery of regulatory motifs in upstream sequences. It also includes annotation and upstream sequence databases for the majority of genes represented on the Affymetrix Arabidopsis 8K GeneChip® array.

When VIZARD was created its name originated from VIsualiZe microARray Data. Now it does much more than visualization of gene expression data, however, we have decided to keep the name.

::DEVELOPER

Nick Moseyko

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

VIZARD

:: MORE INFORMATION

It is available free of charge for educational, research, and not-for-profit purposes. To read full text of the terms under which the program is distributed, click here.

PovChem 2.1.1 – Chemical Visualization & Illustration & POV File Converter

PovChem 2.1.1

:: DESCRIPTION

PovChem is a chemical visualization and illustration program with a new graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration – colors, atom and bond radii, view orientation, etc. It will even calculate and display hydrogen bonds.

PovChem can export the picture in POV-Ray format, which allows you to render the image with a state-of-the-art raytracer, giving high-quality images at any resolution, for anything from web page thumbnails to full-size high-resolution images for journal covers, advertisements, posters, anything!

::DEVELOPER

Paul A. Thiessen

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PovChem

:: MORE INFORMATION

PovChem is now free!Use this key to register your copy of PovChem:
APyUrblJnYZr

RasTop 2.2 – Molecular Visualization Software Adapted for Rasmol

RasTop 2.2

:: DESCRIPTION

RasTop is a molecular visualization software adapted from the program RasMol, which was initially developed by Roger Sayle. RasTop is particularly adapted for educational purposes and for the rapid analysis of macromolecules at the bench.  RasTop wraps a user-friendly graphical interface around the “RasMol molecular engine”. There is no need to type on the command line; each command in the menu generates its own script. Through an extended menu and a command panel, users can manipulate numerous molecules rapidly and learn about them. Work sessions are saved in script format and are fully regenerated with a simple mouse click.

::DEVELOPER

Philippe Valadon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Linux with Wine
  • Mac with Virtual PC

:: DOWNLOAD

RasTop 2.2Version Francaise

:: MORE INFORMATION

RasTop 2.2 is distributed both under the GPL license ad the Rasmol license.  Certain conditions apply to users and to developers to ensure that RasTop remain open source. Please, consult the license.txt and raslic.txt file in the package.