MuGeN has been used successfully on Intel/Linux and Sparc/Solaris platforms. It is not intended for use on Windows machines. Disk space requirements are minimal (less than 7 Mb for the programs/modules and documentation, and an additionnal 25 Mb for the example data) but memory footprint can grow as more feature-rich genomes and/or complex analysis results are loaded. For example, the display of two reasonably-sized microbial genomes (about 4 Mb each) and a box plot of the conserved portions between the two of them consumes about 70 Mb of RAM on an Intel/Linux workstation. Line plots having one or more data points per base can be especially memory-consuming.
MuGeN's programs and modules are all written in Perl. They rely on a set of more or less specialized third-party modules whose list is given in Table 1> (required modules) and Table 2> (optional modules). Notice that these tables only list modules not commonly found in Perl distributions. For a more extensive list of dependencies, see Appendix A>. All of these components are freely available, mostly from CPAN.
MuGeN is available as a gzipped archive. Download the archive in an installation directory and expand its contents by issuing:
gzip -dc mugen-XXXXXXXX.tgz | tar xf -where XXXXXXXX stands for the release number. This will create a subdirectory called mugen-XXXXXXXX containing all of MuGeN's programs, modules and documentation. cd in this directory and type the usual commands for installing a Perl module:
perl Makefile.PL make make install
The executables mugen, mugenb and mugenv are located in a system-wide program directory, like /usr/bin and should be accessible without any specific $PATH settings.
MuGeN relies on a preferences file to fix display and
database connection parameters. By default, it looks for a
file named .mugenrc in the user's
$HOME
directory. If no template file is found
when mugen is run for the first time, a
default template file will be created.
A set of example files, used throughout this document, is available in the mugen-data-XXXXXXXX.tgz archive. This archive can be extracted anywhere and creates a mugen-data-XXXXXXXX directory containing several annotated genomes in GenBank format, as well as some computer analysis results.