Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework

Ancestral genome reconstruction is an important step in analyzing the evolution of genomes. Recent progress in sequencing ancient DNA led to the publication of so-called paleogenomes and allows the integration of this sequencing data in genome evolution analysis. However, the assembly of ancient genomes is fragmented because of DNA degradation over time. Integrated phylogenetic assembly addresses the issue of genome fragmentation in the ancient DNA assembly while improving the reconstruction of all ancient genomes in the phylogeny. The fragmented assembly of the ancient genome can be represented as an assembly graph, indicating contradicting ordering information of contigs.

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