| Summary: | Abstract Background The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. Results We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses. Conclusions We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.
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