Pôle Rhône-Alpes de Bioinformatique Site Doua



LalnView is a graphical program for visualizing local alignments between two sequences (protein or nucleic acids). Sequences are represented by colored rectangles to give an overall picture of the similarities between the two sequences. Blocks of similarity between the two sequences are colored according to the degree of identity between segments.

The program is also able to display sequence features (active site, domain, motif, propeptide, exon, intron, promoter, etc.) along with the alignment. This allows one to make the link between sequence similarity and known functions.

LalnView was developped by Laurent Duret and Jean-Francois Gout.

Use of LalnView

LalnView can be used through the PRABI-Doua server to compare nucleic acid sequences, or through the ExPASy server for protein sequences. Sequences can be entered by the user or extracted from SWISS-PROT, GenBank or EMBL databases.

When using LalnView through these servers, sequence features are automatically extracted from database annotations and displayed with the alignment. A screen shot of the main window is available here. Full text sequences are displayed in a secondary window (see the screen shoot). By clicking on a block, the user can visualize the corresponding local alignment. As domain can be repeated in a sequence, iterative clicking on one block will successively display all the similar blocks that occur in the other sequence. For more details, please read the documentation.

Download LalnView

LalnView can be downloaded through our FTP server. You may also use the following table to directly access the version corresponding to your computer.
If you encounter some problems when using LalnView, please contact Jean-Francois Gout. Any comments or suggestions are welcome.
See the installation instructions.

Logo AppleMacOS (8,9,X)
Logo LinuxLinux on PC
Logo WindowsMS Windows
Logo SolarisSolaris on SPARC

You will find some example data file here and the on-line help file.

Other platforms: LalnView source code (C++) is available here (under the GNU GPL licence). In principle, it should be possible to compile LalnView on any platform. Note however that the source code has been tested only for the platforms mentioned above.

Note for MacOS 8-9 users

LalnView needs a fairly recent (1.6) version of CarbonLib to work. See the Apple CarbonLib update page for update instructions.


If you use LalnView in a published work, please cite the following reference:

Duret, L., Gasteiger, E. and Perrière, G. (1996) LalnView: a graphical viewer for pairwise sequence alignments. Comput. Applic. Biosci., 12, 507-510 [ Abstract ]


LalnView is licensed under the GNU General Public Licence ( ).

LalnView uses the FLTK project ( ) for its user interface.

LalnView uses the PDFlib Lite library ( ) for pdf output under the "Open Source Developer Exemption" of the PDFlib Lite License Agreement.