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The default parameters were: KTUP = 1, window length = 0, topdiag = 1, pairgap = 0.05, matrix BLOSUM, gap-open = 10, end-gaps = 10. gap-extension = 0.05, gap-distance = 0.05.
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note
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The distribution of different types of species in the final set of sequences was as follows: for subunit I, 77 eukaryotic sequences (49 Metazoa, 12 Viridiplantae, 10 Fungi, 2 Rhodophyta, 2 Euglenoza, 1 Myxogastria, 1 Stramenopiles), 13 bacterial sequences (6 Proteobacteria, 4 Firmicutes, 2 Cyanobacteria, 1 Thermus/Deinococcus group), and 2 archaen sequences (1 Euryarchaeota, 1 Crenarchaeota); for subunit II, 196 eukaryotic sequences (157 Metazoa, 2 Alveolata, 3 Euglenozoa, 11 Viridiplantae, 2 Rhodophyta, 1 stramenopiles, 20 Fungi) and 10 bacterial sequences (4 Firmicutes, 3 Proteobacteria, 2 Cyanobacteria, 1 Thermus/Deinococcus group).
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