Propinquity output documentation. The top-level docs are here.
The cleaned_ott directory contains the results of pruning OTT version 3.2draft9 so that the root is 93302 and the taxa flagged with the following flags were removed:
Results: A taxonomy with a total of 3942770 nodes. 3676264 of these are leaves and 266506 internal nodes.
The cleaned_ott.tre file in this directory contains a newick representation of this taxonomy (download newick).
The following table lists the number of OTT Ids pruned by the combination of flags that caused the pruning. We don't list each of the OTT Ids here because the list is extremely long and can make your browser hang. The cleaned_ott.json file in this directory contains the list of pruned Ids (download cleaned_ott.json).
| Combination of flags | # of nodes pruned |
|---|---|
| barren | 1 |
| barren,hidden | 2 |
| barren,hidden,inconsistent | 1 |
| barren,hidden,inconsistent,major_rank_conflict | 1 |
| barren,hidden,major_rank_conflict | 29 |
| barren,hidden,major_rank_conflict,merged | 4 |
| barren,hidden,merged | 4 |
| barren,hidden,was_container | 8 |
| barren,hybrid | 2 |
| barren,inconsistent | 18 |
| barren,inconsistent,major_rank_conflict | 2 |
| barren,major_rank_conflict | 11 |
| barren,major_rank_conflict,merged | 1 |
| barren,merged | 3 |
| barren,not_otu,was_container | 8 |
| barren,was_container | 1 |
| empty-after-higher-taxon-tip-prune | 37 |
| environmental | 2 |
| environmental,hidden | 73 |
| environmental,hidden,not_otu | 25 |
| environmental,inconsistent | 14 |
| environmental,inconsistent,not_otu | 9 |
| environmental,merged | 2 |
| environmental,merged,not_otu | 2 |
| environmental,not_otu | 36 |
| environmental,not_otu,was_container | 1 |
| hidden | 11 |
| hidden,inconsistent | 8 |
| hidden,major_rank_conflict | 13 |
| hidden,merged | 2 |
| hidden,not_otu | 6 |
| hidden,was_container | 8 |
| higher-taxon-tip | 2188 |
| hybrid | 1 |
| hybrid,not_otu | 2 |
| hybrid,not_otu,was_container | 1 |
| inconsistent | 30 |
| inconsistent,not_otu | 1 |
| major_rank_conflict | 2 |
| major_rank_conflict,merged | 2 |
| merged | 1 |
| merged,not_otu | 1 |
| not_otu | 9 |
| not_otu,viral | 3 |
| not_otu,was_container | 1 |
| was_container | 4 |