JaDis is a program for computing distances between nucleic acid
allows specific comparison of coding sequences, of non-coding
sequences, or of
coding and non-coding sequences.
JaDis set-up and start
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
the directories where program are searched the path leading to the java
binary. Ask your system administrator if you don't know how to
PATH environment variable for UNIX.
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.
procedure differs following your operating system:
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
This archive does not need to be expanded to install JaDis. Retrieve
this file using
mode of your FTP client and save it in the directory
you want to run the program. Retrieve the shell file
and edit it by replacing the string
the path leading to the directory containing the two files jadis.jar
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:
Use of JaDis
Most usual sequence alignment formats can be read: FASTA, CLUSTAL and
the program is entirely mouse-driven.
Many distance can be computed with JaDis including nucleic distances
NCDF, Jukes and Cantor, Two-parameters Kimura, Galtier and Gouy, Tamura
and protein distances (Ka, Ks, Kas). The features of those distances
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
dissymmetry. At last, G+C frequencies can be computed.
JaDis results can be saved into text files that can be directly used
or statistical software in order to analyse and
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.
Goncalves I, Robinson M, Perriere G, Mouchiroud D.
JaDis: computing distances between nucleic acid sequences.
Bioinformatics. 1999 May;15(5):424-5.