3. Installation/Download

phyloMOD runs under Linux, any distribution.
DOWNLOAD

It is distributed as a compressed .tar.gz archive so you need to copy the source files to your local computer and untar/ungzip them from the command line:

% gunzip phyloMOD.tar.gz

% tar xvf phyloMOD.tar

You should obtain a new directory, phyloMOD, containing the perl script phyloMOD.pl and some annotation examples.

phyloMOD.pl can be used from any directory so you can copy wherever you need it.

Beeing a Perl script phyloMOD.pl does not require any installation. Tough, the following software needs to be installed in your system:

• Perl
• Mysql (with database 'test' accessible to any user).
• Grace, also know as xmgr.
• bl2seq, part of BLAST package from NCBI.

I assume Perl is installed under /usr/bin/perl otherwise you need to go into phyloMOD.pl and change the first line with the proper path to your Perl interpreter (you can find the path issuing the following command: 'whereis perl'). This is not needed if you launch phyloMOD.pl invoking first the Perl interpreter (e.g. % perl phyloMOD.pl).