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

The cleaned_ott directory contains the results of pruning OTT version 3.0draft6 so that the root is 93302 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 3137818 nodes. 2918983 of these are leaves and 218835 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 63
barren,hidden,major_rank_conflict,merged 10
environmental,inconsistent,not_otu 9
barren,hidden,inconsistent,major_rank_conflict 3
barren,extinct,inconsistent,major_rank_conflict 1
not_otu,viral 1
environmental,hidden,not_otu 25
not_otu,was_container 6
barren,major_rank_conflict 12
extinct,merged 1
hybrid,not_otu 1
barren,was_container 12
extinct,hidden,merged 5
barren,hidden,merged 13
extinct 1
barren,extinct,merged 26
barren,extinct,hidden,inconsistent 15
extinct,hidden,major_rank_conflict 41
extinct_inherited,major_rank_conflict 21
barren,extinct,hidden,merged 14
barren,extinct,hidden,major_rank_conflict,merged 3
extinct,hidden 2
extinct_inherited 2
hybrid 43
barren,inconsistent 1
barren,hidden 22
barren,extinct,hidden 3
barren,extinct,was_container 1
environmental,not_otu 41
hidden 2
barren,extinct,major_rank_conflict 134
barren,not_otu,was_container 8
merged 1
hidden,not_otu 6
barren,merged 4
merged,not_otu 1
barren,extinct,major_rank_conflict,merged 29
barren,major_rank_conflict,merged 1
higher-taxon-tip 3204
environmental,inconsistent 14
barren,inconsistent,major_rank_conflict 10
hidden,merged 1
environmental,hidden 73
barren,extinct 1
inconsistent,not_otu 2
hidden,major_rank_conflict 1
barren,hidden,was_container 4
hidden,was_container 2
inconsistent 2
was_container 4
barren,extinct_inherited 1
major_rank_conflict 1
environmental 18
environmental,not_otu,was_container 1
barren,hidden,major_rank_conflict 18
barren,extinct,hidden,major_rank_conflict 596
not_otu 4
extinct,major_rank_conflict 619
environmental,merged 2
extinct,hidden,inconsistent 1
barren 1
barren,hidden,inconsistent 116
barren,extinct_inherited,hidden 1
environmental,merged,not_otu 2
extinct_inherited,hidden 1
extinct,was_container 1