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If you manage phylogenetic data, Bio::NEXUS can make your life easier with a library and ready-made tools to manipulate and visualize NEXUS files (see http://www.molevol.org/nexplorer and http://search.cpan.org/dist/Bio-NEXUS/doc/Tutorial.pod).
plsync is a lightweight remote file synchronization software much like rsync, written entirely in Perl. It features a Perl module, a command line tool and a Network daemon. It is aiming at low ressource consumption (RAM, CPU) and maximum portability.
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Oscar Notify is a small client<->server tool kit that implements the Oscar protocol. It allows you to connect to the ICQ/AIM network and use a small command line tool to send messages to a desired icq number. Works great with Nagios
NWBal is a command line tool for viewing your Natwest on-line banking balance and mini statements for all your accounts. It includes an email reporting facility for daily reports will soon have graphing capability for viewing historical data.