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

The bumped_ott directory a copy of the version of OTT that may have some extinct (often incertae sedis) taxa moved toward the root of the tree.

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

If there is an "edits" property in the JSON file at ../cleaned_ott/move_extinct_higher_log.json. If that property does not exist, then the taxonomy files in this directory will be links to the files in ../subott_dir.

See https://github.com/OpenTreeOfLife/reference-taxonomy/wiki/Interim-taxonomy-file-format for documentation of the OTT format.

Any *.pickle files are Python pickle artifacts of reading the taxonomy. They can be deleted because they can be regenerated from the primary OTT files.

The taxonomic structure in the files in this directory will determine the phylogenetic interpretation of names in the rest of the synthesis run.

Results:

• cleaned_ott.json is a JSON summary (often a large file that can be hard to look at in a browser) that lists the reasons different taxa were pruned. The file is composed from 2 different files (which are rarely of direct interest to end-users): flagged_in_cleaned.json and cleaned_ott_pruned_nonflagged.json/
• cleaned_not_updated_ott.tre is a newick representation of the taxonomy.
• cleaned_ott_with_hiddenbarren.tre is another representation of the taxonomic tree. This file contains higher taxa that lack descendants. Such taxa are pruned from the cleaned_not_updated_ott.tre form.
• cleaned_ott.tre is the newick representation of the taxonomy to be used in subsequent steps.