JaDis is a program for computing distances between nucleic acid sequences. It allows specific comparison of coding sequences, of non-coding sequences, or of coding and non-coding sequences.

JaDis set-up and start

Java installation

The first thing you need to do is to install a Java Virtual Machine (JVM) on your computer if you don't have it yet. 

In the case of  UNIX machines, you will need to add to the list of the directories where program are searched the path leading to the java binary. Ask your system administrator if you don't know how to configure the PATH environment variable for UNIX.

JaDis Installation

Note that the source code of JaDis classes can be downloaded here. The version of JaDis for Windows and MacOS8->9 platforms is available on the pôle Bio-Informatique Lyonnais site : http://pbil.univ-lyon1.fr/software/jadis.html.

The set-up procedure differs following your operating system:

MacOS X:
Simply download the JaDis.app.tar.gz file and put it in your "Applications" folder. Decompact the archive with the command line `tar zxvf JaDis.app.tar.gz` and then you have in the folder a clickable application.

All the Java classes required to run JaDis are stored into a java archive (jar) file named jadis.jar. This archive does not need to be expanded to install JaDis. Retrieve this file using the binary mode of your FTP client and save it in the directory where you want to run the program. Retrieve the shell file JaDis.csh and edit it by replacing the string /Applications/jadis by the path leading to the directory containing the two files jadis.jar and Help.

JaDis start

The procedure to run the program also differs following your computer. On Macintosh computers, simply double-click on the JaDis or JaDis.bin file. On UNIX computers, go to the directory where the JaDis.csh file is stored and type: ./JaDis.csh.

Use of JaDis

Most usual sequence alignment formats can be read: FASTA, CLUSTAL and MASE and the program is entirely mouse-driven. Many distance can be computed with JaDis including nucleic distances (SDF, NSDF, NCDF, Jukes and Cantor, Two-parameters Kimura, Galtier and Gouy, Tamura and Nei) and protein distances (Ka, Ks, Kas). The features of those distances are described more precisely in the help file of the JaDis distribution.

Other characteristics of the substitution process include transition and transversion rates and an index of substitution dissymmetry. At last, G+C frequencies can be computed.

JaDis results can be saved into text files that can be directly used by spreadsheet or statistical software in order to analyse and visualise the results. All distances can also be saved in a PHYLIP format.

If you encounter some problems with JaDis, please contact  Isabelle Gonçalves. Any comments or suggestions are welcome.

Reference :

Goncalves I, Robinson M, Perriere G, Mouchiroud D.
JaDis: computing distances between nucleic acid sequences.
Bioinformatics. 1999 May;15(5):424-5.