{"__v":0,"_id":"5799e7b9c0c50c22008d6f28","category":{"project":"57618347b65324200072d6a5","version":"57618347b65324200072d6a8","_id":"579ca6f3d46f960e0029a8ec","__v":0,"sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-07-30T13:09:07.617Z","from_sync":false,"order":9999,"slug":"glossary","title":"Glossary"},"parentDoc":null,"project":"57618347b65324200072d6a5","user":"57617c8caa540f3600bfed20","version":{"__v":8,"_id":"57618347b65324200072d6a8","project":"57618347b65324200072d6a5","createdAt":"2016-06-15T16:33:11.587Z","releaseDate":"2016-06-15T16:33:11.587Z","categories":["57618347b65324200072d6a9","5761912d207db7170022fbe9","57619455a7c9f729009a74e0","576e8ae1f37ab41700147471","5797b8e5209a6e0e00b8321b","57989a8817ced017003c4c69","579ca6f3d46f960e0029a8ec","579ca703fefb1d0e00c94f06"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"blobtools v0.9.19","version_clean":"0.9.19","version":"0.9.19"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-07-28T11:08:41.841Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":0,"body":"* Taxonomy of a sequence is calculated at each [taxonomic rank](doc:taxonomic-rank) by [tax-rules](doc:tax-rule) \n\n* The taxonomy of a sequence is represented by three values:  \n * ```taxonomic name``` : the taxonomic name at that taxonomic rank (calculated by the tax-rule)\n * ```score``` : the score of the taxonomic name (calculated by the tax-rule)\n * ```c-index``` : count of alternative candidates for taxonomic name\n\n\n* if the [hits file(s)](doc:taxonomy-file) contained no hits for a given sequence, the taxonomy is set to:\n *  ```taxonomic name``` = \"no-hit\"\n * ```score``` = 0.0\n * ```c-index``` = None\n\n\n* if the taxonomy is \"unresolved\" (due to ```[--min_diff FLOAT]``` or two equally well scoring taxonomic names) the taxonomy is set to:\n *  ```taxonomic name``` = \"unresolved\"\n\n\n* if a taxID does not have a node at a given [taxonomic rank](doc:taxonomic-rank), the taxonomy of the next highest annotated rank gets used and the suffix \"-undef\" is appended, e.g.:\n * 9823 (Sus scrofa) does not posess a node at rank \"order\", order is set to \"Chordata-undef\"\n\n\n* The [taxonomy](doc:taxonomy) of a sequence determines its colour in a [blobplot](doc:blobplot)/[covplot](doc:covplot)","excerpt":"","slug":"taxonomy","type":"basic","title":"taxonomy"}
* Taxonomy of a sequence is calculated at each [taxonomic rank](doc:taxonomic-rank) by [tax-rules](doc:tax-rule) * The taxonomy of a sequence is represented by three values: * ```taxonomic name``` : the taxonomic name at that taxonomic rank (calculated by the tax-rule) * ```score``` : the score of the taxonomic name (calculated by the tax-rule) * ```c-index``` : count of alternative candidates for taxonomic name * if the [hits file(s)](doc:taxonomy-file) contained no hits for a given sequence, the taxonomy is set to: * ```taxonomic name``` = "no-hit" * ```score``` = 0.0 * ```c-index``` = None * if the taxonomy is "unresolved" (due to ```[--min_diff FLOAT]``` or two equally well scoring taxonomic names) the taxonomy is set to: * ```taxonomic name``` = "unresolved" * if a taxID does not have a node at a given [taxonomic rank](doc: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](doc:taxonomy) of a sequence determines its colour in a [blobplot](doc:blobplot)/[covplot](doc:covplot)