Hi IGV devs,
A feature I would find very useful (and I hope others too!) is the ability to view multiple genomes in the same session through the lens of a multiple sequence alignment of the genomes/transcripts. Here, a bam/bed/bw file would be aligned to a specific genome, and because the genomes/transcripts would be aligned to each other, the alignment/coverage of each sample could be easily compared across organisms.
If there is already a tool that does this, or if there is a roundabout way to do this in IGV, I'll be happy if someone can share their knowledge.
Best,
Joe