Heikki Lehvaslaiho wrote: > > Depreciated methods should not be called within bioperl. They will > print a warning if called. There is a remote chance that ClustalW or > TCoffee modules contains some, but I do not have the programs > installed. Somebody else please check. > Heikki Neither Clustalw.pm nor Tcoffee.pm use the deprecated methods, so everything should be fine. Regards - Peter