JaDis

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 Windows or 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 Windows or UNIX.

JaDis Installation

The whole directory containing the JaDis distribution can be reached at URL:

<ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/jadis>

Note that the source code of JaDis classes can be downloaded here.

For Windows and Unix computers, 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. You have also to get the Help and Help2 files to be able to access the on-line help when running JaDis. Note that these files need to be retrieved using the ascii mode of your client. The set-up procedure differs following your operating system:

  1. Windows:
    Retrieve the command file JaDis.bat and edit it by replacing all occurrences of string C:\Applications\jadis by the complete path leading to the directory containing the files jadis.jar and Help.

  2. Unix/Linux:
    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.

  3. MacOS 8.0 --> 9.2:
    On Macintosh computers, depending on the JVM installed, the JaDis installation process varies greatly. If you use the MacOS Runtime for Java (MRJ) virtual machine, simply download the JaDis.bin file. For this purpose, use the MacBinary II mode of your FTP client and save the file in the directory where the jadis.jar and Help files are already stored.

    4. Note that JaDis runs well with MacOS 8.0/8.1 associated with MRJ 2.0 but this version of MRJ is NOT fully compatible with MacOS 8.5 (scrollbars are not functional). So if you have this version of MacOS installed on your computer, it is better to wait for the availability of MRJ 2.1. Also JaDis has not been tested on Macintoshes running a version of MacOS prior to 8.0.

  4. MacOS X
    Simply download the JaDis.app.tar file and put it in your "Applications" folder. Expand the archive either with the command line tar xvf JaDis.app.tar or Stuffit Expander, and then you have in the folder a clickable application.

JaDis start

The procedure to run the program also differs following your computer. On Windows and Macintosh computers, simply double-click either on the JaDis.bat JaDis.bin (MacOS 8.0 --> 9.2) or JaDis file (MacOS X). 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 Help2 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 like excell or statview 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 Guy Perrière (installing) or Isabelle Gonçalves (using). Any comments or suggestions are welcome.

If you have problems or comments...

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