Propinquity output documentation. The top-level docs are here.
The cleaned_phylo contains the results of pruning problematically mapped tips from phylogenetic inputs. See the Procedure section below for more details on the process.
Next step: The next step in phylogeny processing is to choose exemplars for tips that are mapped to higher taxa (see ../exemplified_phylo/index.html). First, though, we pre-process the Open Tree Taxonomy (see ../cleaned_ott/index.html).
Results: There were 2,034 nonempty trees after cleaning. The files of interest in this directory are:
| JSON log of pruning | pruned newick | induce taxonomy newick for pruned |
|---|---|---|
^ot:inGroupClade set to a node, then that node and all of
its descendants will be retained and the "outgroup" will be pruned off the tree.otu that does not have a ot:^ottId property, these nodes are pruned as "unmapped_otu""unrecognized_ott_id""flagged""mapped_to_taxon_containing_other_mapped_tips"^ot:isTaxonExemplar or because it had a node
id that is "lower" in lexicographic sort than any other node Id."became_trival""higher-taxon-tip" (note that an input tree can have higher taxa as tips, but if just
taxa lack children in the taxonomy, they are "barren" in the OTT sense and should be removed)."empty-after-higher-taxon-tip-prune""replaced_by_arbitrary_node""replaced_by_exemplar_node". (If there were multiple exemplar nodes, then the same sorting as described above
was chosen to choose among them)"revised_ingroup_node".