Propinquity output documentation. The top-level docs are here.

The cleaned_ott directory contains the results of pruning OTT version 2.10draft11 so that the root is 212201 and the taxa flagged with the following flags were removed:

Next step: Choose exemplars for tips in phylogenies that are mapped to higher taxa. See ../exemplified_phylo/index.html.

Results: A taxonomy with a total of 44360 nodes. 38420 of these are leaves and 5940 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
empty-after-higher-taxon-tip-prune 3
hybrid,infraspecific 4
not_otu 1
barren,was_container 7
extinct 2
barren,environmental,was_container 35
barren,extinct,hidden,merged 1
extinct,hidden 3
hybrid 3
barren,inconsistent 9
not_otu,unclassified 2
barren,hidden 25
barren,extinct,hidden 29
hidden 1
barren,extinct,major_rank_conflict 4
infraspecific 11
barren,unclassified,was_container 4
hybrid,not_otu,unclassified 1
barren,merged 39
barren,major_rank_conflict,merged 1
higher-taxon-tip 27
barren,extinct 8
hybrid,unclassified 2
environmental 16
barren,hidden,major_rank_conflict 14
barren,extinct,hidden,major_rank_conflict 303
unclassified 3788
extinct,major_rank_conflict 9
hybrid,not_otu 7
barren 117