The current implementation of alignments and (ultimately) variants is too strict about preventing people from using it on internal nodes. We have to do a lot of faddling around like this to get it t work, and even then it still doesn't work on the distributed version because it has a disconnected node (which we're not interested in).

This is core functionality for sc2ts users, so we want to make this possible. Even if it's just a flag saying "do this anyway" that's better than the current status.

Related:

• Support missing data in alignments #1896
• Implement Tree.has_isolated_samples #1908

Can you have a look and see what the options are please @benjeffery ?