Home
Navigation
Home
Sweet home.
The projects
The people
Jobs
Contact
Search
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

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
    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

  • Clustal
    • New Clustal webpage
    • Clustal Omega
      "Please note that Clustal Omega is currently a command line-only tool, and is only suitable for aligning protein sequences, not DNA or RNA."
      Download
    • New ClustalW/ClustalX webpage
      Download, starting with version 2.1.
    • ClustalX - a new windows interface for the ClustalW multiple sequence alignment program. New ClustalX Version download here (FTP, up to version 2.0.12).
      I suggest to compress the EXE file with UPX, which will reduce its size to about 29% and will make the program startup faster.
    • ClustalX Old and much smaller ClustalX version 1.83 direct download from here.
    • ClustalW download (1) (2) (FTP server)
  • T-Coffee - Computation of a Multiple Sequence Alignment
  • Muscle - MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation
  • GeneDocGeneDoc - A Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows. Download page for the version 2.7.000 (March 2, 2007).
    Old page with the version # 2.6.02 as of July, 2001. Download page.
    local Download the lastest version 2.7.001 with the EXE-file form May 27, 2007.

    GeneDoc version 2.7 has a new file header format that is NOT backwards compatable. This means that files saved by 2.7 will not be able to be read by earlier versions. If you share your files with other GeneDoc users, they will need to update to 2.7 as well.
    This header change was made to fix a bug with large files.

  • Jalview
  • CHROMA CHROMA
    CHROMA is a tool for generating annotated multiple sequence alignments in a convenient format for publication.
    Literature :
    CHROMA: consensus-based colouring of multiple alignments for publication
    Leo Goodstadt and Chris P. Ponting
  • OctopusOctopus 4.1 (a graphical BLAST/FASTA parser) - from Patrick Durand, local Download
  • HoKAlign - A GUI under Windows for several free command line driven sequence alignment programs
  • FASTA BLAST Scan is a program for processing FASTA and BLAST nucleotide sequences alignments. You can use it to transfer your BLAST output file into a "multiple FASTA" file. The lastest version on the webpage is 2.1 but you can find version 2.3 (July 6, 2007) here (direkt download version 2.3).

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

Jump to

Software
!!!