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The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogeniesβa challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time. We present a new whole-genome based approach to infer phylogenies that is alignment- and reference-free.
In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de Bruijn graph is constructed, and information on common subsequences is extracted to infer phylogenetic splits. The introduced new methodology for large-scale phylogenomics shows high potential.
Application to different datasets confirms robustness of the approach. A comparison to other state-of-the-art whole-genome based methods indicates comparable or higher accuracy and efficiency. A common task in comparative genomics is the reconstruction of the evolutionary relationships of species or other taxonomic entities, their phylogeny. Thus, more and more genomes are published in an unfinished state, i. Hence, traditional approaches for phylogenetic inference can often not be applied, because they are based on the identification and comparison of marker sequences, which relies on computing multiple alignmentsβan NP-hard task in theory, and in practice even heuristics are often too slow.