Comparing two highly similar genomes
I have two highly similar mammalian genomes at the chromosome level, one is a wild species and another is a domestic species. For finding the species-specific sequence (unconserved sequence), I aligned together using the "nucmer" (from MUMmer4), but it sounds that this tool is not suitable for this comparison; because when I manually checked the part of genome sequence in wild species without any counterpart sequence within domestic species using blast, this tool can find a sequence with high identity in the domestic species, unlike the "nucmer" tool. Could you please let me know any appropriate tool for comparing these two highly similar genomes?
Thanks in advance
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