Figure 4

Barcodes in feature space. The x-axis is the average of variations of the 4-mer frequencies across a whole genome across all 4-mers, and the y-axis measures the similarity level among all 1000-bp partitioned fragments of the genome, each represented as a 136-dimensional vector of 4-mer frequencies; Specifically, for each genome, we build a minimum spanning tree [27] based on the 4-mer frequency vectors for its sequence fragments and their distances. The y-axis is the averaged weight (distance) of all edges in the minimum spanning tree. The green dots represent prokaryotes (586 genomes), the blue ones for eukaryotes (83 chromosomes), the red ones for plastids (101 genomes with lengths > 20,000 bps), the brown ones for plasmids of prokaryotic genomes (237 plasmids > 20,000 bps) and the black for mitochondria (120 genomes with lengths > 20,000 bps).