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).
- easy to install: perl -MCPAN -e 'install Bio::NEXUS'
- manipulate data in NEXUS files using a command-line tool (nextool.pl)
- write a custom script to select (exclude) OTUs from matrix AND tree
- write a custom script to re-root a tree (or a thousand trees at once)
- generate scalable PS image of data and tree (nexplot.pl)
Thanks for updates ;)