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Caner Bagci, David Bryant, Banu Cetinkaya and Daniel H. Huson (University of Tübingen, Tübingen, Germany)
Microbiome studies involve constructing draft genomes of unknown organisms using sequencing, assembly, and contig-binning methods. To determine the phylogenetic context of a draft genome, we provided an interactive approach as part of SplitstreeCE. This approach, given a set of query sequences, quickly analyzes the phylogenetic context. In the preprocessing step, mash sketch of each reference genome of GTDB is computed, a Bloom filter to each internal node of the taxonomy, that represents the reference genomes under that node, is assigned. Then, the mash sketch of the draft genome is computed against the precomputed data to obtain pairwise distances to the most similar reference genomes. The neighbor-net method is then applied, the resulting phylogenetic context is displayed as a novel phylogenetic outline. Phylogenetic outline is more general than a phylogenetic tree and allows for vagueness in the placement of draft genomes which is suitable to indicate context. This approach is not limited to phylogenetic context and can serve as a visualization of neighbor-net results in other analyses as well. This is joint work with Caner Bagci, Dave Bryant and Daniel Huson.