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With this file it is possible to bootstrap the new alignment of N+1 sequences (Pfam alignment plus query sequence) in precisely the same manner, so the NxN precalculated distances are valid for the (N+1)x(N+1) distance matrix.
For an overview, see Table 1. From the 17,847 A. thaliana domain sequences matching a Pfam family, 14,905 (84%) could be analyzed with RIO using the precalculated distances.
Following the above rules, pairwise distances were precalculated for 2384 alignments from a total of 3071 in Pfam 6.6 (75 alignments were too short and 612 alignments contained less than six sequences from species in the master species tree).
Correspondingly, from the 12,314 C. elegans domain sequences matching a Pfam family, 11,287 (92%) could be analyzed with RIO using the precalculated distances.