Taxonomy

• Taxonomy of a sequence is calculated at each taxonomic rank by tax-rules
• The taxonomy of a sequence is represented by three values:
• taxonomy : the NCBI taxonomy name at that taxonomic rank (calculated by the taxrule)
• score : the score of the taxonomy (calculated by the taxrule)
• c-index : count of alternative candidates for taxonomy
• if the hits file(s) contained no hits for a given sequence or the score did not surpass --min_score FLOAT], the taxonomy is set to no-hit
• if the taxonomy is "unresolved" (due to [--min_diff FLOAT] or two equally well scoring taxonomic names) the taxonomy is set to unresolved
• if a taxID does not have a node at a given taxonomic rank, the taxonomy of the next highest annotated rank gets used and the suffix -undef is appended, e.g.:
• 9823 (Sus scrofa) does not posess a node at rank "order", order is set to "Chordata-undef"
• The taxonomy of a sequence determines its colour in a blobplot/covplot