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
PATH environment variable for Windows or UNIX.
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:
C:\Applications\jadisby the complete path leading to the directory containing the files jadis.jar and Help.
/Applications/jadisby the path leading to the directory containing the two files jadis.jar and Help.
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.
tar xvf JaDis.app.taror Stuffit Expander, and then you have in the folder a clickable application.
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.
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