Importing trees with unspecified rank levels

[davve2]

How to deal with input trees with no clear rank order or given levels (QIIME includes p__, s__ etc) but a standard CanSNPer tree does not (for example). Should FlexTaxD assume that the top X order follow a certain level structure, or should it require "--skip_rank" or a given file with "translated" ranks? Or should default behaviour be to create a number series for the levels?

A;B;C;D
vs
d__A,c__B,o__C,f__D