/usr/bin/phyml-beagle is in phyml 3:3.2.0+dfsg-7+b1.
This file is owned by root:root, with mode 0o777.
It is a symlink to /usr/bin/../lib/phyml/bin/phyml-beagle
/usr/bin/../lib/phyml/bin/phyml-beagle