Welcome to Wise2.2 You must set your WISECONFIGDIR to the config directory before using the programs: in (t)csh: setenv WISECONFIGDIR PREFIX/share/wise/ in (ba)sh: export WISECONFIGDIR=PREFIX/share/wise/ To try an example: cd PREFIX/share/examples/wise genewise road.pep human.genomic [Replace 'PREFIX' above with the actual installation prefix, which by default is '/usr/local'.]