I have prediction for 10 CDS from 10 genes respectively.

The CDS are nearly identical, while the gene sequences (i.e. intronic portions) are not.

I have checked to see whether positions of intron-exon boundaries are conserved, indeed they are.

Now I want to align the entire gene sequences, so that I can "visualize" both the highly conserved regions (corresponding to exons) and the less conserved intronic / non-exon regions.

Based on this visualization, my goal is to identify regions on the alignment where I can design primers to, so I can distinguish PCR template sequences based on length and/or sequence differences.

I have successfully performed 1 CDS <=> 1 gene alignment with SPLIGN

But I wonder what tool I may use to align

a. 1 CDS to multiple genes (works when CDS is identical or near identical)

b. multiple CDS and multiple genes (required when CDS are not 100% identical across related genes)

I also have available the predicted aa sequence from the predicted CDS (though that is trivial info that can be easily inferred even otherwise)

I am considering GenePainter for my tasks a & b listed above, but via this post, I hope to gather opinions / ideas on other solutions for my visualization and primer design requirements. Thanks!