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Sequence embedding for fast construction of guide trees for multiple sequence alignment

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Figure 1 Tree Distances. Tree distances of SparseMap and mBed guide trees from full matrix guide trees for the BAliBase benchmark set (386 families), using the Robinson-Foulds metric
Table 1: mBed performance on the ten biggest Pfam/HOMSTRAD families.
Figure 2 Complexity of Embedding. Total time required to compute a full pair-wise distance matrix (red) is plotted against time taken to embed sequences (blue) for each entry in the HOMSTRAD/Pfam dataset (containing up to 10,000 sequences per entry).
Figure 3 Times for embedding up to 300,000 tRNA sequences. Number of calls to the d(x, y) distance function made during computa-tion of a full pair-wise distance matrix (red), plotted against number of sequences for random subsets of Rfam entry RF00005 whi
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