I failed using MEGA, BioEdit, Jalview and CodonCode, how can I do this?
This is a comment rather than answer - but not enough rep
I don't think you'll find any tool to do this exactly as you want - how is it going to decide what's a dot and what's a letter (or a space,N or whatever) if you have multiple ambiguities or even an even number of alignments split 50:50?
Wouldn't be hard to code something which prints the whole column if it consists of non-identical nucleotides, else dots. Would be easy in R, could probably even do it in Excel without too much effort and no need to use VBA.