I'm wondering if have a tool that identifies non-conserved regions between 2 eukaryotic genomes (like pan-genomic tools for prokaryotes, that are capable of identify accessory genes).
At the simplest level, you could do local alignments between 2 genomes with something like mummer, find all the conserved regions, then simply flip all the coordinates you got back to find all the regions which were less conserved than that threshold.
Hi I used to use the ECR browser for this type of question, you can find the details at https://ecrbase.dcode.org/. Just be aware that it was last updated in 2008! But this might be useful to you.
I'm gonna read about, thanks
Why not use Orthofinder? Give a couple of files containing protein sequences for each species and let it work its magic through.
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