This is the directory for the Bioperl C compiled Extensions. The main author for this is Ewan Birney To install... cd into Bio/Ext/Align go perl Makefile.PL make make test (should print out alignment on STDERR) make install (probably need root permissions). Although these extensions can be called by themselves, they really need the main bioperl distribution to drive them. The modules which do this are Bio::Tools::pSW - makes smith waterman alignments Bio::SearchDist - deals with EVD fitting of extreme value distributions For more information on how to use these modules, read their own documentation (go perldoc Bio::Tools::pSW ...)