Parameters for diploid ancient tetraploid

[ghost]

Hello,

I have a phased assembly of a diploid organism. It happens it is also an ancient tetraploid (old genome duplication). I would like to show those alignments on a dot plot (the allelic pairs and the ohnolog pairs). But I can't seem to find minimap2 parameters sensitive enough. All it returns, with the option -X, are the self hits of tandem repeats.

To illustrate I have chromosome quartets A1 A2 and A3 A3 I would like to see the alignment A1 A2 A3 A4 (A1 - A3-4 will have lower identity for instance).

Ohnolog pairs maybe have 20% divergence.

Can minimap2 do that?

thank you

[ghost]

EDIT: could be my dotplot program, Dgenies, does not represent exactly the things the way I want, not sure it's a minimap2 issue any more. I am leaving it open because I am still interested in advices in parameters.

[lh3]

What is the minimap2 command line you are using?