GMV 1.0c-beta – Genome Map Viewer

GMV 1.0c-beta

:: DESCRIPTION

GMV (Genome Map Viewer) is a tool that compares gene order in two or more genomes and displays the results in the form of the concentric ring display of Moore et al.(1995) and Gale and Devos (1998). This display shows the relative positions of linkage blocks in a set of species, where these blocks have been proposed on the basis of conservation of gene order across the species being examined. In cereals these blocks are often based on rice.

::DEVELOPER

 DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

  GMV

:: MORE INFORMATION

 

CDTree 3.1 – Protein Domain Hierarchy Viewer and Editor

CDTree 3.1

:: DESCRIPTION

CDTree is a powerful tool to aid in the classification of protein sequences and investigate their evolutionary relationships;

::DEVELOPER

The NCBI Structure Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

CDTree

:: MORE INFORMATION

Citation:

Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH.
CDD: a conserved domain database for interactive domain family analysis.
Nucleic Acids Res. 2007;35 (Database Issue):D237-40.

PrIMETV 1.5.6 – PrIME Tree Viewer

PrIMETV 1.5.6

:: DESCRIPTION

PrIMETV is a program that can visualize tree-within-tree phenomena such as gene/species tree reconciliations. Output can be given in a range of formats.

::DEVELOPER

Stockholm Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows with cygwin

:: DOWNLOAD

PrIMETV

:: MORE INFORMATION

Citation:

Sennblad B et al (2007) primetv: a viewer for reconciled trees. BMC Bioinformatics 8, 148

Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0 – Multiple Sequence Alignment , Viewer & Quality Assessment

Kalign 2.03 / Kalignvu 2.1 / Mumsa 1.0

:: DESCRIPTION

Kalign is a fast and accurate multiple sequence alignment software.

Kalignvu is an lightweight viewer for multiple sequence alignments and phylogenetic trees.

Mumsa is a program to assess the quality of multiple sequence alignments.

::DEVELOPER

Dr. Erik Sonnhammer

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Kalign ;  Kalignvu / Mumsa

:: MORE INFORMATION

Citation:

Kalign – an accurate and fast multiple sequence alignment algorithm.
Lassmann T. and Erik L.L. Sonnhammer (2005)
BMC Bioinformatics, 6:298

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment.
Lassmann T. and Erik L.L. Sonnhammer (2006)
Nucleic Acids Research, 34:W596-W599

ANTHEPROT 3D 1.0.162- Molecule Viewer to look at PDB files

ANTHEPROT 3D 1.0.162

:: DESCRIPTION

Antheprot 3D is a molecular graphics program intended for the visualisation of proteins, nucleic acids from RCSB archive. The program is aimed at display, teaching and generation of publication quality images.

The program reads in a molecule coordinate file (PDB format) and interactively displays the molecule on the screen in a variety of color schemes and molecule representations. Currently available representations include wireframes, sticks, spheres, ball and stick, atom labels and distances. PDB files that are available either locally (Ctrl+O or File=>Open) or distantly at “POLE Bioinformatique Lyonnais” (Ctrl+I) or File=> PBIL URL can be loaded directly into AntheProt3D.

The program is made of 3 different windows:

  • A 3D view window which allows the user to interactively move the molecule
  • A group selection panel for group selection
  • A text window for provinding the user the list of clicked atoms, information (F2) and PHI, PSI values

A Ramachandran interactive plot is also available

Features

  • Alpha trace, wireframe, space filled,Balla nd Sticks, Sticks and surface mode.
  • Full support of clipping (“molecule slicing”)
  • Full support of stereo (side by side, anaglyph or quad buffer stereo)
  • Interactive Ramachandran plot
  • Hydrogen addition or removal by reduce
  • Selection of amino acids by group, chain or within a sphere
  • Surface viewer for MSMS files (Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996).Biopolymers, 38 (3), 305-320.
  • Ribbon or cylinder mode from Molscript program (P. J. Kraulis, (1991) Journal of Applied Crystallography 24, pp 946-950.)
  • Support for Delphi electrostatic potential Rocchia, W.; Alexov, E.; Honig, B. (2001) J Phys. Chem. 105, 6507-6514

::DEVELOPER

Pr Gilbert Deléage at France Institute of Biology and Chemistry of Proteins

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

ANTHEPROT 3D 1.0.162

:: MORE INFORMATION

ANTHEPROT3D album

If you use ANTHEPROT on PC, please cite one of the following references :

Deleage G, Combet C, Blanchet C, Geourjon, C
ANTHEPROT: An integrated protein sequence analysis software with client/server capabilities?
(2001) COMPUTERS IN BIOLOGY AND MEDICINE 31 (4): 259-267

Chemis3D 2.89b – Java 3D Molecular Viewer Applet

Chemis3D 2.89b

:: DESCRIPTION

Chemis3D is a Java Applet which renders virtual 3D molecular models within a Web document. It is specially designed for open interactive molecular visualization on the Internet or via an intranet. Molecular structures can be manipulated in real-time and rendered in various styles and appearances.

Chemis3D is a small applet running well on any Java-enabled browser and requiring no specialized plug-in nor professional applications.

Features

  • Real-time manipulation and fast 3D rendering.
  • Wide variety of molecular representations including special styles and color coding schemes for proteins and nucleic acids .
  • Enhanced interface using popumenu and key shortcuts .
  • Multi-models display and molecular animation capabilities.
  • Measuring and analysing tools.
  • Support of the most popular molecular data formats :Brookhaven Protein DataBank (*.pdb).MSC XMol files (*.xyz).MDL molfiles (*.mol).

::DEVELOPER

Didier COLLOMB

:: SCREENSHOTS

:: REQUIREMENTS

  • Java-enabled browser

:: DOWNLOAD

Chemis3D 2.89b

:: MORE INFORMATION

Chemis3D MAY BE FREELY USED FOR PERSONNAL, ACADEMIC AND NON-COMMERCIAL PURPOSES, IN AGREEMENT WITH THE FOLLOWING RESTRICTIONS.