This site contains some DNA programs I have been working on.
Show Graph shows a graph of sequence variation amongst some sequences. It was originally designed for human, but I have put up some SARS-CoV-2 (Covid 19) alignments. I was looking for variations more complex than just SNPs or simple indels, or correlations between them, but didn't find them. However it is a fine visualizer for the SNPs. For looking at deduced phylogenetic relationships, I recommend Nextstrain.
Compare allows a simple comparison of the sequences of a small number of similar virus sequences.
Coming Real Soon Now: A human genome browser using a similar graph structure for structural variants.
For all these tools, I recommend reading the tutorial linked at the top of the page. I strongly recommend using a large screen.
I am interested long term in making a genome alignment tool for human dealing well with known structural variation.
If you have ideas for collaboration email me at username andrew at the domain andrewconway.org