In the case of Windows or Unix machines, you will need to add to the list of
the directories where programs 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.
All the Java classes required to run FamFetch are stored into a java archive file named
This archive does not need to be expanded to install FamFetch. For all types of computers
and systems, you must retrieve this file using the binary mode of your FTP client
and save it in the directory where you want to have the program located. You have also to
file to be able to access the on-line help when running FamFetch. Note that
this file need to be retrieved using the ascii mode of your client. The
set-up procedure then differs following your operating system:
FamFetch.batand edit it by replacing all occurrences of string
C:\Appli\FamFetchby the path leading to the directory containing the files
FamFetch.binfile. For this purpose, use the MacBinary II mode of your FTP client and save the file in the directory where the
Helpfiles are already stored. Note that you can download the latest version of the MRJ using the address listed in the Java installation section.
FamFetch runs well with MacOS 8.0 to 9.2.2 associated with MRJ 2.1 but it has not been tested on Macintoshes running a version of MacOS prior to 8.0. Also, do not use versions of MRJ prior to 2.1.
FamFetch-2.0-OSX.tgzand double click on it to decompress. The directory contain the FamFetch executable.
FamFetch.cshand edit it by replacing the string
/Appli/FamFetchby the path leading to the directory containing the two files
FamFetchfile. On Unix computers, go to the directory where the
FamFetch.cshfile is stored and type
FamFetch.csh. Another possibility is to copy or move this shell file to one of the directories that are listed in the
When the program is started for the first time, it is initialized with
default parameters, particularly a default server is used. A common thing
to do is to change the preferences in a way to use the closest server
available. To do that, select the option
Prefs in the
File menu and use one of the possibilities listed in this
table. It shows the main places where the server has been installed:
Server: names of the server, Port: port number on which the HTTP service is running, Script: path to and name of the CGI-script that is started when the server receives a query, Databases: list of the available homologous genes databases available.
here. More documentation on the search of phylogenetic trees in databases is available here
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