Biotools lists (a collection of links to other
Working with "complex" sequence files
Graphics (view and process)
Places to look for more biology related software
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
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.
RasMol - RasWin
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.
Linux, Mac, Solaris) - DNA sequence trace viewer
Can also show the RAW data.
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
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
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.
- An extensive list of software for
ALIGNMENTS at molbiol-tools.ca
New Clustal webpage
"Please note that Clustal Omega is currently a command line-only tool, and is only suitable for
aligning protein sequences, not DNA or RNA."
New ClustalW / ClustalX webpage
Download, starting with
ClustalX - a new
windows interface for the ClustalW multiple sequence alignment program. New ClustalX Version download
here (FTP, up to version
I suggest to compress the EXE file with UPX, which
will reduce its size to about 29% and will make the program startup faster.
Old and much smaller ClustalX version 1.83 direct
download from here.
ClustalW download (1)
(2) (FTP server)
Computation of a Multiple Sequence Alignment
Muscle - MUSCLE stands for MUltiple Sequence Comparison by
GeneDoc - 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.
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.
CHROMA is a tool for generating annotated multiple sequence alignments in a
convenient format for publication.
CHROMA: consensus-based colouring of multiple alignments for publication
Leo Goodstadt and Chris P. Ponting
Octopus 4.1 (a graphical BLAST/FASTA parser) - from Patrick Durand, Download
HoKAlign - A GUI under Windows for several free command line driven sequence alignment
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.
TreeView - Tree drawing software for Apple Macintosh and Windows
ATV (A Tree Viewer) (a part of forester) -
a phylogenetic tree display tool, is now called
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
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).
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"
-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
Dendroscope - An
interactive viewer for large phylogenetic trees (Java based)
SplitsTree 4 -
computing evolutionary networks from molecular sequence data (Java based)
- MSTgold: create a MST (minimum spanning tree) from any kind of data, with bootstrapping.
The output file can be directly processed by GraphViz to produce a graphic.
A selection of software can be found on alternativeto.net!