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Bio-Tools
Useful links to servers on the net
that provide bioinformatics services
and links to free bioinformatics software.

Google search
of the CMBN web pages.

Bio-Tools

Free Software

Biotools lists (a collection of links to other listings)

Oligo Software

3D Modelling

  • QMol (An OpenGL based molecular viewer for Windows 95/NT/00 and X Windows)

    Qmol is a program for viewing molecular structures and animating molecular trajectories. Originally based on the molview demo program by Mark Kilgard (from his book, Programming OpenGL for the X Window System) and inspired by the Xmol program. Qmol is similar to programs like VMD , MolMol , weblab, Swiss-Pdb Viewer, MolScript, RasMol, RasMol 2.7, Rastop 1.3, Rastop 2, gOpenMol and ICM, but opts for fast, high quality rendering of molecules with an easy to use user interface.

  • Jmol - a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems
  • PyMol is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation.
  • DeepView - Swiss-PdbViewer
  • RasMol - RasWin
  • RasTop
  • QuteMol

Sequencing

  • Chromas Lite (Win) - Opens chromatogram files from Applied Biosystems and Amersham MegaBace DNA sequencers. Opens SCF format chromatogram files created by ALF, Li-Cor, Visible Genetics OpenGene, Beckman CEQ 2000XL and CEQ 8000, and other sequencers.
  • Ridom TraceEdit (Win, Linux, Mac) Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format. Incorrect base calls can be edited and saved. TraceEdit is freely available and designed to operate on Windows, MacOS X and UNIX platforms.
  • FinchTV (Win, Linux, Mac, Solaris) - DNA sequence trace viewer
    Can also show the RAW data.
    Download Windows version
  • ApE can read ABI sequencing trace files
  • ABIVIEW in the EMBOSS package can displey ABI trace files
  • BioEdit has ABI and SCF trace viewing, editing and conversion
  • Sequence Scanner Software from ABI
    The free Sequence Scanner Software enables you to view, edit, print and export sequence data generated using the Applied Biosystems Genetic Analyzers. The software generates graphically expressive reports on results.
    (direkt download link)
  • CodonCode's TraceViewer
    You can download the program from the www.genecore.embl.de site.
    CodonCode's TraceViewer is a Java program that allow you to see, print, and edit DNA sequencing traces. If the traces were processed with Phred and therefore contain base call qualities, TraceViewer allows you to see Phred quality values.

Alignment

Phylogeny

  • TreeView - Tree drawing software for Apple Macintosh and Windows
  • JavaATV (A Tree Viewer) (a part of forester) - a phylogenetic tree display tool, is now called
    Archaeopteryx
    Java has to be installed!
    • obsolete - Download Version 1.92 from FTP
      Under Windows OS you can start the program version 1.92 with a batch file in the program folder containing: 
      java -cp ATVapp.jar ATVapp %1
    • obsolete - New webpage here! Latest version: ATV 4.00 ALPHA 5 (2007-06-05)
      For starting versions 3 and 4 use: 
      start /B javaw.exe -jar forester.jar %*
      You may also create a shortcut with this string (without "start /B", which avoids the DOS command window).
    • Archaeopteryx homepage
      For starting you may use a batch files containing something like this (no line breaks): 
      java -Xms32m -Xmx512m -cp "C:\Program Files\forester-atv\forester.jar"
org.forester.archaeopteryx.Archaeopteryx
-c "C:\Program Files\forester-atv\_aptx_configuration_file" %1

    Information from the Archaeopteryx webpage:

    Archaeopteryx has only basic editing capabilities. If comprehensive editing functions are required, Dendroscope is a recommended alternative — which, similar to Archaeopteryx, can visualize large trees (with more than 20 000 nodes). TreeDyn is another tool with extensive editing capabilities. Drawtree and Drawgram from PHYLIP, as well as TreeView, are well established and widely used programs for tree visualization and printing. Phylodendron provides web based printing capabilities. Geneious is an integrated bioinformatics software suite with nice tree visualization capabilities.
  • Dendroscope - An interactive viewer for large phylogenetic trees (Java based)
  • SplitsTree 4 - computing evolutionary networks from molecular sequence data (Java based)

Working with "complex" sequence files

etc.

Graphics (view and process)

Places to look for more biology related software

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