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"Species Hypothesis" view

• Reference sequence (RefS) – serves as a name anchor for the Species Hypothesis and is chosen manually by an expert to define the SH. It may originate from any biological sample, viz. herbarium specimen, living culture, soil, water, air, tissue of other organism, etc. The RefS forms a part of the name of the full name of the SH is thus used for scientific communication.
• Representative sequence (RepS) - when RefS are not available (has not been designated manually), a representative sequence (RepS) is chosen automatically from the most common sequence type in the SH. All SHs have a RepS. For SHs for which a RefS has been designated, the RefS takes precedence over the RepS. The RepS are shown in green font in the SH pages (e.g., https://unite.ut.ee/sh/SH005769.07FU).
• Threshold values - each threshold value shows minimum distance between two sister Species Hypotheses (SH). Threshold value 1.0% means that two sequences belong into different SHs if their ITS2 sequences are more than 1% different. However, they fall into single SH under 1% threshold value if third sequence, which is 0.5% different from both sequences, becomes available. In other words, two sister SHs fall into single SH under specific threshold value if the distance between two most similar sequences in sister SHs are more similar than this specific threshold value requires.
• Distribution of distances - pairwise distances for ITS sequences were calculated using the pairwise.seqs command in mothur package (http://www.mothur.org/wiki/Pairwise.seqs). The exact parameters used for the program were - countends=F, match=1, mismatch=-3.