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Updated: Nov 16, 2025

Methodology for Accurate Detection of Mitochondrial DNA Methylation
Published on: May 20, 2018
HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades
Federico Plazzi1, Guglielmo Puccio1, Marco Passamonti1
1Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
Abstract:
Mitochondrial chromosomes have diversified among eukaryotes and many different architectures and features are now acknowledged for this genome. Here we present the improved HERMES index, which can measure and quantify the amount of molecular change experienced by mitochondrial genomes. We test the improved approach with ten molecular phylogenetic studies based on complete mitochondrial genomes, representing six bilaterian Phyla. In most cases, HERMES analysis spotted out clades or single species with peculiar molecular synapomorphies, allowing to identify phylogenetic and ecological patterns. The software presented herein handles linear, circular, and multi-chromosome genomes, thus widening the HERMES scope to the complete eukaryotic domain.
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