currently the --outgroup and --outgroup_crop commands work when the input tree is unrooted. When someone tries to use them with a rooted tree they are just ignored (the delimitation is done on the original rooted tree) and there is no error message.
There should either be an error message saying that the tree is already rooted or, preferably, re-root the tree according to the taxa defined by the user.
currently the
--outgroupand--outgroup_cropcommands work when the input tree is unrooted. When someone tries to use them with a rooted tree they are just ignored (the delimitation is done on the original rooted tree) and there is no error message.There should either be an error message saying that the tree is already rooted or, preferably, re-root the tree according to the taxa defined by the user.