/usr/bin/cd-hit-2d-para is in cd-hit 4.6.1-2012-08-27-2.
This file is owned by root:root, with mode 0o777.
It is a symlink to /usr/bin/../lib/cd-hit/cd-hit-2d-para.pl
/usr/bin/../lib/cd-hit/cd-hit-2d-para.pl