Times for embedding up to 300,000 tRNA sequences. Number of calls to the d(x, y) distance function made during computation of a full pair-wise distance matrix (red), plotted against number of sequences for random subsets of Rfam entry RF00005 which contains 381,602 tRNA sequences. We only show the number of calls up to 40,000 sequences. In blue we show the times for embedding subsets up to 300,000 sequences in size. The full data set takes 40 minutes to embed.