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Figure 3 | Genome Biology

Figure 3

From: The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes

Figure 3

Gingr visualization of 826 P. difficile genomes aligned with Parsnp. The leaves of the reconstructed phylogenetic tree (left) are paired with their corresponding rows in the multi-alignment. A genome has been selected (rectangular aqua highlight), resulting in a fisheye zoom of several leaves and their rows. A SNP density plot (center) reveals the phylogenetic signature of several clades, in this case within the fully-aligned hpd operon (hpdB, hpdC, hpdA). The light gray regions flanking the operon indicate unaligned sequence. When fully zoomed (right), individual bases and SNPs can be inspected.

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